Compositions comprising HIV envelopes to induce CH235 lineage antibodies

ABSTRACT

In certain aspects the invention provides HIV-1 immunogens, including HIV-1 envelope selections from individual CH505, and methods for swarm immunizations using combinations of HIV-1 envelopes.

This application is a U.S. National Stage application under 35 U.S.C. § 371 of International Patent Application No. PCT/US2017/020249, filed Mar. 1, 2017 which claims the benefit of and priority to U.S. Provisional Application No. 62/302,017 filed on Mar. 1, 2016 and U.S. Provisional Application No. 62/403,503 filed on Oct. 3, 2016. The entire contents of each of these applications are incorporated herein by reference in their entirety.

This invention was made with government support under Center for HIV/AIDS Vaccine Immunology-Immunogen Design grant UM1-AI100645 from the NIH, NIAID, Division of AIDS. The government has certain rights in the invention. The United States government also has rights in this invention pursuant to Contract No. DE-AC52-06NA25396 between the United States Department of Energy and Los Alamos National Security, LLC for the operation of Los Alamos National Laboratory.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Aug. 20, 2020, is named 1234300_300_US2_SL.txt and is 1,240,139 bytes in size.

TECHNICAL FIELD

The present invention relates in general, to a composition suitable for use in inducing anti-HIV-1 antibodies, and, in particular, to immunogenic compositions comprising envelope proteins and nucleic acids to induce cross-reactive neutralizing antibodies and increase their breadth of coverage. The invention also relates to methods of inducing such broadly neutralizing anti-HIV-1 antibodies using such compositions.

BACKGROUND

The development of a safe and effective HIV-1 vaccine is one of the highest priorities of the scientific community working on the HIV-1 epidemic. While anti-retroviral treatment (ART) has dramatically prolonged the lives of HIV-1 infected patients, ART is not routinely available in developing countries.

SUMMARY OF THE INVENTION

In certain embodiments, the invention provides compositions and method for induction of immune response, for example cross-reactive (broadly) neutralizing Ab induction. In certain embodiments, the methods use compositions comprising “swarms” of sequentially evolved envelope viruses that occur in the setting of bnAb generation in vivo in HIV-1 infection.

In certain aspects the invention provides compositions comprising a selection of HIV-1 envelopes and/or nucleic acids encoding these envelopes as described herein for example but not limited to Selections as described herein. Without limitations, these selected combinations comprise envelopes which provide representation of the sequence (genetic) and antigenic diversity of the HIV-1 envelope variants which lead to the induction and maturation of the CH103 and CH235 antibody lineages. In certain embodiments the selections of envelopes comprise envelopes which show differential binding to an antibody or antibodies from CH103 and CH235 lineages (FIGS. 14-16, FIGS. 17-24). Non-limiting embodiments of various selections of immunogens are described in Example 3. In certain embodiments, these compositions are used in immunization methods as a prime and/or boost.

In certain embodiments the selections of envelopes comprise envelopes which show differential binding to an antibody or antibodies from CH103 and CH235 lineages (FIGS. 14-16, FIGS. 17-24). In certain aspects, the invention provides a kit comprising a combination/selection of immunogens of Example 3. In some embodiments the selection of immunogens is selection F, selection G, or selection H. In some embodiments the kit comprises instructions on how to carry out the immunization regimen. In some embodiments the kit comprises instructions on administration of the selection of immunogens as a prime or boost as part of a prime/boost immunization regimen. In certain aspects, the invention provides a kit comprising any one of the immunogens of Example 3, or in selection F, G, or H and instructions on how to carry out an immunization regimen with the immunogen of the kit, including which immunogen(s) are a prime immunization and which immunogen(s) comprise a boost immunization. In some embodiments the kit comprises instructions on administration of the immunogen as a prime or as a boost as part of a prime/boost immunization regimen. In some embodiments the immunogen could be administered sequentially or additively.

In certain aspects, the invention provides a kit comprising Env M5, M11, 20.14, 30.20, 30.12, 30.21 30.23, 30.25, 30.28, 53.25, 53.29, 53.31, 78.15, 100.B6 and/or 136.B18. In some embodiments the kit comprises instructions on how to carry out the immunization regimen, including which immunogen(s) are a prime immunization and which immunogen(s) comprise a boost immunization. In some embodiments the kit comprises instructions on administration of the immunogen as a prime or as a boost as part of a prime/boost immunization regimen.

In some embodiments, the kit comprises Env M5, M11, w20.14, w30.20 and/or w136.B18 and instructions on administration of the immunogen as a prime or boost as part of a prime/boost immunization regimen with M5, M11, w20.14, w30.20 and/or w136.B18, including which immunogen(s) are a prime immunization and which immunogen(s) comprise a boost immunization In some embodiments, the kit comprises Env M5, w30.25, w53.25 and/or w53.29 and instructions on administration of the immunogen as a prime or boost as part of a prime/boost immunization regimen with M5, w30.25, w53.25 and/or w53.29, including which immunogen(s) are a prime immunization and which immunogen(s) comprise a boost immunization.

In one aspect the invention provides selections of envelopes from individual CH505, which selections can be used in compositions for immunizations to induce lineages of broad neutralizing antibodies. In certain embodiments, there is some variance in the immunization regimen; in some embodiments, the selection of HIV-1 envelopes may be grouped in various combinations of primes and boosts, either as nucleic acids, proteins, or combinations thereof. In certain embodiments the compositions are pharmaceutical compositions which are immunogenic. In certain embodiments, the compositions comprise amounts of envelopes which are therapeutic and/or immunogenic.

In one aspect the invention provides a composition for a prime boost immunization regimen comprising any one of the envelopes described herein, or any combination thereof wherein the envelope is a prime or boost immunogen. In certain embodiments the composition for a prime boost immunization regimen comprises one or more envelopes from FIGS. 14-16, FIGS. 17-24, Example 3, or from immunogen selection F, selection G, or selection H. In some embodiments, the composition for a prime boost immunization regimen comprises one or more envelopes M5, M11, 20.14, 30.20, 30.12, 30.21 30.23, 30.25, 30.28, 53.25, 53.29, 53.31, 78.15, 100.B6 and/or 136.B18.

In one aspect the invention provides a composition comprising any one of the envelopes described herein, or any combination thereof—for example but not limited to selections in Examples and FIGS. 14, 15, 16, 17-24. In other aspects, the invention provides use of these selections of envelopes in methods to induce an immune response. In non-limiting embodiments the envelope selections induce antibodies in the CH235 lineage, for example antibody CH557, (described in Example 8).

In some embodiments, CH505 M11 Env is administered first as a prime, followed by a mixture of a next group of Envs. In some embodiments, grouping of the envelopes is based on their binding affinity for the antibodies expected to be induced. In some embodiments, grouping of the envelopes is based on chronological evolution of envelope viruses that occurs in the setting of bnAb generation in vivo in HIV-1 infection. In some embodiments Loop D mutants could be included in either prime and/or boost. In some embodiments, the composition comprises an adjuvant. In some embodiments, the composition and methods comprise use of agents for transient modulation of the host immune response.

In one aspect the invention provides a composition comprising nucleic acids encoding HIV-1 envelope which is a loop D mutant, e.g. M11 or any other suitable D loop mutant or combination thereof, e.g. M11 and M5.

In another aspect the invention provides a method of inducing an immune response in a subject comprising administering a composition comprising HIV-1 envelope M11 and/or M5 as a prime in an amount sufficient to induce an immune response, wherein the envelope is administered as a polypeptide or a nucleic acid encoding the same. A method of inducing an immune response in a subject comprising administering a composition comprising HIV-1 envelope M11 and M5 as a prime in an amount sufficient to induce an immune response, wherein the envelope is administered as a polypeptide or a nucleic acid encoding the same.

In certain embodiments the methods comprise administering any of the selection listed in Example 3. In certain embodiments the methods comprise administering Envs M5, M11, 20.14, 30.28, 30.23, and/or 136.B18. In certain embodiments the methods comprise administering Envs M5, M11, 20.14, 30.20, 30.23, and/or 136.B18. In certain embodiments the methods comprise administering Envs M5, M11, 20.14, 30.20, 30.12, and/or 136.B18. In certain embodiments the methods comprise administering envelopes M5, 30.25, 53.25, and/or 53.29.

In certain embodiments the methods further comprise administering a composition comprising any one of HIV-1 envelope M11, w020.14, w030.28, w078.15, w053.31 or any combination thereof as a boost, wherein the envelope is administered as a polypeptide or a nucleic acid encoding the same.

In certain embodiments the methods comprise administering a composition comprising any one of HIV-1 envelope M11, M5, w020.14, w030.28, w078.15, w053.31 or any combination thereof as a boost, wherein the envelope is administered as a polypeptide or a nucleic acid encoding the same.

In another aspect the invention provides a method of inducing an immune response in a subject comprising administering a composition comprising HIV-1 envelope M11, M5, w020.14, w030.28, w078.15, w053.16, w030.21, w078.33, w100.B6, w053.31 or any combination thereof as a prime and/or boost in an amount sufficient to induce an immune response, wherein the envelope is administered as a polypeptide or a nucleic acid encoding the same.

In certain embodiments, the compositions contemplate nucleic acid, as DNA and/or RNA, or proteins immunogens either alone or in any combination. In certain embodiments, the methods contemplate genetic, as DNA and/or RNA, immunization either alone or in combination with envelope protein(s).

In certain embodiments the nucleic acid encoding an envelope is operably linked to a promoter inserted an expression vector. In certain aspects the compositions comprise a suitable carrier. In certain aspects the compositions comprise a suitable adjuvant.

In certain embodiments the induced immune response includes induction of antibodies, including but not limited to autologous and/or cross-reactive (broadly) neutralizing antibodies against HIV-1 envelope. Various assays that analyze whether an immunogenic composition induces an immune response, and the type of antibodies induced are known in the art and are also described herein.

In certain aspects the invention provides an expression vector comprising any of the nucleic acid sequences of the invention, wherein the nucleic acid is operably linked to a promoter. In certain aspects the invention provides an expression vector comprising a nucleic acid sequence encoding any of the polypeptides of the invention, wherein the nucleic acid is operably linked to a promoter. In certain embodiments, the nucleic acids are codon optimized for expression in a mammalian cell, in vivo or in vitro. In certain aspects the invention provides nucleic acids comprising any one of the nucleic acid sequences of invention. In certain aspects the invention provides nucleic acids consisting essentially of any one of the nucleic acid sequences of invention. In certain aspects the invention provides nucleic acids consisting of any one of the nucleic acid sequences of invention. In certain embodiments the nucleic acid of the invention, is operably linked to a promoter and is inserted in an expression vector. In certain aspects the invention provides an immunogenic composition comprising the expression vector.

In certain aspects the invention provides a composition comprising at least one of the nucleic acid sequences of the invention. In certain aspects the invention provides a composition comprising any one of the nucleic acid sequences of invention. In certain aspects the invention provides a composition comprising at least one nucleic acid sequence encoding any one of the polypeptides of the invention.

In certain aspects the invention provides a composition comprising at least one nucleic acid encoding HIV-1 envelope M11, M5, w020.14, w030.28, w078.15, w053.16, w030.21, w078.33, w100.B6, w053.31 or any combination thereof. Non-limiting examples of combinations are shown in Example 2.

In certain embodiments, the compositions and methods employ an HIV-1 envelope as polypeptide instead of a nucleic acid sequence encoding the HIV-1 envelope. In certain embodiments, the compositions and methods employ an HIV-1 envelope as polypeptide, a nucleic acid sequence encoding the HIV-1 envelope, or a combination thereof.

The envelope used in the compositions and methods of the invention can be a gp160, gp150, gp145, gp140, gp120, gp41, N-terminal deletion variants as described herein, cleavage resistant variants as described herein, or codon optimized sequences thereof. In certain embodiments the composition comprises envelopes as trimers. In certain embodiments, envelope proteins are multimerized, for example trimers are attached to a particle such that multiple copies of the trimer are attached and the multimerized envelope is prepared and formulated for immunization in a human. In certain embodiments, the compositions comprise envelopes, including but not limited to trimers as particulate, high-density array on liposomes or other particles, for example but not limited to nanoparticles. In some embodiments, the trimers are in a well ordered, near native like or closed conformation. In some embodiments the trimer compositions comprise a homogenous mix of native like trimers. In some embodiments the trimer compositions comprise at least 85%, 90%, 95% native like trimers.

The polypeptide contemplated by the invention can be a polypeptide comprising any one of the polypeptides described herein. The polypeptide contemplated by the invention can be a polypeptide consisting essentially of any one of the polypeptides described herein. The polypeptide contemplated by the invention can be a polypeptide consisting of any one of the polypeptides described herein. In certain embodiments, the polypeptide is recombinantly produced. In certain embodiments, the polypeptides and nucleic acids of the invention are suitable for use as an immunogen, for example to be administered in a human subject.

In certain embodiments the envelope is any of the forms of HIV-1 envelope. In certain embodiments the envelope is gp120, gp140, gp145 (i.e. with a transmembrane), gp150. In certain embodiments, gp140 designed to form a stable trimer (See Table 1, FIGS. 22-24, Example 9 for non-limiting examples of sequences of stable trimer designs). In certain embodiments envelope protomers from a trimer which is not a SOSIP timer. In certain embodiment the trimer is a SOSIP based trimer wherein each protomer comprises additional modifications. In certain embodiments, envelope trimers are recombinantly produced. In certain embodiments, envelope trimers are purified from cellular recombinant fractions by antibody binding and reconstituted in lipid comprising formulations. See for example WO2015/127108 titled “Trimeric HIV-1 envelopes and uses thereof” which content is herein incorporated by reference in its entirety. In certain embodiments the envelopes of the invention are engineered and comprise non-naturally occurring modifications.

In certain embodiments, the envelope is in a liposome. In certain embodiments the envelope comprises a transmembrane domain with a cytoplasmic tail embedded in a liposome. In certain embodiments, the nucleic acid comprises a nucleic acid sequence which encodes a gp120, gp140, gp145, gp150, gp160.

In certain embodiments, where the nucleic acids are operably linked to a promoter and inserted in a vector, the vectors is any suitable vector. Non-limiting examples, include, VSV, replicating rAdenovirus type 4, MVA, Chimp adenovirus vectors, pox vectors, and the like. In certain embodiments, the nucleic acids are administered in NanoTaxi block polymer nanospheres. In certain embodiments, the composition and methods comprise an adjuvant. Non-limiting examples include, AS01 B, AS01 E, gla/SE, alum, Poly I poly C (poly IC), polyIC/long chain (LC) TLR agonists, TLR7/8 and 9 agonists, or a combination of TLR7/8 and TLR9 agonists (see Moody et al. (2014) J. Virol. March 2014 vol. 88 no. 6 3329-3339), or any other adjuvant. Non-limiting examples of TLR7/8 agonist include TLR7/8 ligands, Gardiquimod, Imiquimod and R848 (resiquimod). A non-limiting embodiment of a combination of TLR7/8 and TLR9 agonist comprises R848 and oCpG in STS (see Moody et al. (2014) J. Virol. March 2014 vol. 88 no. 6 3329-3339).

In certain aspects the invention provides a cell comprising a nucleic acid encoding any one of the envelopes of the invention suitable for recombinant expression. In certain aspects, the invention provides a clonally derived population of cells encoding any one of the envelopes of the invention suitable for recombinant expression. In certain aspects, the invention provides a sable pool of cells encoding any one of the envelopes of the invention suitable for recombinant expression.

In certain aspects, the invention provides a recombinant HIV-1 envelope polypeptide from Table 1, wherein the polypeptide is a non-naturally occurring protomer designed to form an envelope trimer. The invention also provides nucleic acids encoding these recombinant polypeptide. Non-limiting examples of amino acids and nucleic acid of such protomers are shown in FIGS. 22-24.

In certain aspects the invention provides a recombinant trimer comprising three identical protomers of an envelope from Table 1. In certain aspects the invention provides an immunogenic composition comprising the recombinant trimer and a carrier, wherein the trimer comprises three identical protomers of an HIV-1 envelope listed in Table 1. In certain aspects the invention provides an immunogenic composition comprising nucleic acid encoding these recombinant HIV-1 envelope and a carrier.

In certain aspects the invention provides a selection of HIV-1 envelopes or any suitable form of a nucleic acid encoding HIV-1 envelope for use in an immunization regimen, wherein the selections of envelopes comprises envelopes M5, M11, w20.14, w30.20, w30.12, and w136.B18 (Selection F, e.g. listed in FIG. 18A) or any combination thereof, envelopes M5, w30.25, w53.25, and w53.29 (Selection G, e.g. FIG. 20) or any combination thereof, envelopes M5, w30.20, w20.14, and w30.12 (Selection H, e.g. FIG. 21) or any combination thereof. In certain aspects the invention provides a selection of HIV-1 envelopes for immunization wherein the HIV-1 envelope is a loop D mutant envelope M5 and/or M11. In certain embodiments the prime is M5.

In certain aspects the invention provides a selection of nucleic acids encoding HIV-1 envelopes for immunization wherein the nucleic acid encodes a gp120 envelope, gp120D8 envelope, a gp140 envelope (gp140C, gp140CF, gp140CFI) as soluble or stabilized protomer of a SOSIP trimer, a gp145 envelope, a gp150 envelope, or a transmembrane bound envelope.

In certain aspects the invention provides a selection of HIV-1 envelopes for immunization wherein the HIV-1 envelope is a gp120 envelope or a gp120D8 variant. In certain embodiments a composition for immunization comprises protomers that form stabilized SOSIP.III trimers.

In certain embodiments, the compositions for use in immunization further comprise an adjuvant.

In certain embodiments, wherein the compositions comprise a nucleic acid, the nucleic acid is operably linked to a promoter, and could be inserted in an expression vector.

In certain aspects, the invention provides a kit comprising a combination/selection of immunogens of from Table 1, wherein the polypeptide is a non-naturally occurring protomer designed to form an envelope trimer. In certain aspects, the invention provides a kit comprising a combination/selection of immunogens of from FIGS. 22-24. In some embodiments the kit comprises instructions on how to carry out the immunization regimen, including which immunogen(s) are a prime immunization and which immunogen(s) comprise a boost immunization. In some embodiments the kit comprises instructions on administration of the selection of immunogens as a prime or boost as part of a prime/boost immunization regimen. In certain aspects, the invention provides a kit comprising any one of the immunogens from Table 1, wherein the polypeptide is a non-naturally occurring protomer designed to form an envelope trimer and instructions on how to carry out an immunization regimen with the immunogen of the kit. In some embodiments the kit comprises instructions on administration of the immunogen as a prime or as a boost as part of a prime/boost immunization regimen. In some embodiments the immunogen could be administered sequentially or additively. In certain aspects, the invention provides a kit comprising a combination/selection of immunogens of from FIGS. 22-24.

In one aspect the invention provides a composition for a prime boost immunization regimen comprising one or more envelopes from Table 1, wherein the polypeptide is a non-naturally occurring protomer designed to form an envelope trimer, wherein the envelope is a prime or boost immunogen. In one aspect the invention provides a composition for a prime boost immunization regimen comprising one or more envelopes from FIGS. 22-24 wherein the envelope is a prime or boost immunogen.

In certain aspects the invention provides methods of inducing an immune response in a subject comprising administering a composition comprising any suitable form of a nucleic acid(s) encoding an HIV-1 envelope(s) in an amount sufficient to induce an immune response from one or more of the following groups: (a) the selection of envelopes M5, M11, w20.14, w30.20, w30.12, and w136.B18 (Selection F, e.g. listed in FIG. 18A) or any combination thereof, (b) envelopes M5, w30.25, w53.25, and w53.29 (Selection G, e.g. FIG. 20) or any combination thereof, (c) envelopes M5, w30.20, w20.14, and w30.12 (Selection H, e.g. FIG. 21) or any combination thereof and wherein the administration step can alternatively, or in addition, comprise administering an HIV-1 polypeptide(s) in an amount sufficient to induce an immune response from one or more of the following groups: (a) envelopes M5, M11, w20.14, w30.20, w30.12, and w136.B18 (Selection F, e.g. listed in FIG. 18A) or any combination thereof; (b) envelopes M5, w30.25, w53.25, and w53.29 (Selection G, e.g. FIG. 20) or any combination thereof, (c) envelopes M5, w30.20, w20.14, and w30.12 (Selection H, e.g. FIG. 21) or any combination thereof. In certain embodiments, the composition comprises M5 or a nucleic acid encoding M5 that is administered as a prime immunogen. In certain embodiments, the methods further comprise administering M11 or a nucleic acid encoding M11. In certain embodiments, the methods further comprise administering HIV-1 envelope w20.14 or a nucleic acid encoding HIV-1 envelope w20.14, followed by administering HIV-1 envelope w30.20 or a nucleic acid encoding HIV-1 envelope w30.20, and followed by administering HIV-1 envelope w30.12 or a nucleic acid encoding HIV-1 envelope w30.12. In certain embodiments, the methods further comprise administering HIV-1 envelope w136.B18 or a nucleic acid encoding HIV-1 envelope w136.B18.

In certain embodiments, the methods further comprise administering HIV-1 envelope w30.25 or a nucleic acid encoding HIV-1 envelope w30.25, HIV-1 envelope w53.25 or a nucleic acid encoding HIV-1 envelope w53.25, HIV-1 envelope w53.29 or a nucleic acid encoding HIV-1 envelope w53.29.

In certain embodiments, the nucleic acid encodes a gp120 envelope, gp120D8 envelope, a gp140 envelope (gp140C, gp140CF, gp140CFI) as soluble or stabilized protomer of a SOSIP trimer, a gp145 envelope, a gp150 envelope, or a transmembrane bound envelope. In certain embodiments, the polypeptide is gp120 envelope, gp120D8 envelope, a gp140 envelope (gp140C, gp140CF, gp140CFI) as soluble or stabilized protomer of a SOSIP trimer, a gp145 envelope, a gp150 envelope, or a transmembrane bound envelope.

In certain aspects, the invention provides a method of inducing an immune response in a subject comprising administering a composition comprising envelope CH505 T/F, followed by envelope w53.16, followed by envelope w78.33 and followed by envelope w100.B6, wherein each composition comprises the envelope as a trimer. In certain embodiments of the method the selection of immunogens is administered as nucleic acids.

In certain embodiments, the methods comprise administering an adjuvant. In certain embodiments, the methods comprise administering an agent which modulates host immune tolerance. In certain embodiments, the administered polypeptide is multimerized in a liposome or nanoparticle. In certain embodiments, the methods comprise administering one or more additional HIV-1 immunogens to induce a T cell response. Non-limiting examples include gag, nef, pol, etc.

In certain aspects, the invention provides a recombinant HIV-1 Env ectodomain trimer, comprising three gp120-gp41 protomers comprising a gp120 polypeptide and a gp41 ectodomain, wherein each protomer is the same and each protomer comprises portions from envelope BG505 HIV-1 strain and gp120 polypeptide portions from a CH505 HIV-1 strain and stabilizing mutations A316W and E64K, (see e.g. FIG. 23). In certain embodiments, the trimer is stabilized in a prefusion mature closed conformation, and wherein the trimer does not comprise non-natural disulfide bond between cysteine substitutions at positions 201 and 433 of the HXB2 reference sequence. Non-limited examples of envelopes contemplated as trimers are listed in Table 1. In some embodiments, the amino acid sequence of one monomer comprised in the trimer is shown in FIG. 22-24. In some embodiments, the trimer is immunogenic. In some embodiments the trimer binds to any one of the antibodies PGT145, PGT151, CH103UCA, CH103, VRC01, PGT128, or any combination thereof. In some embodiments the trimer does not bind to antibody 19B and/or 17B.

In certain aspects, the invention provides a pharmaceutical composition comprising any one of the recombinant trimers of the invention. In certain embodiments the compositions comprising trimers are immunogenic. The percent trimer in such immunogenic compositions could vary. In some embodiments the composition comprises 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% stabilized trimer.

In certain aspects the invention provides any suitable form of a nucleic acid encoding a HIV-1 envelope from the selections of envelopes listed in FIG. 14A (envelopes M5, M11, 20.14, 30.28, 30.23. and 136.B18), FIG. 15A (envelopes M5, M11, 20.14, 30.20, 30.23. and 136.B18), FIG. 16A (envelopes M5, M11, 20.14, 30.20, 30.12. and 136.B18), FIG. 18A (envelopes M5, M11, 20.14, 30.20, 30.12, and 136.B18), FIG. 20 (M5, 30.25; 53.25; and 53.29), FIG. 21 (M5, w30.20, w20.14, w30.12), or any combination thereof. In certain embodiments the envelopes bind preferentially to an antibody or antibodies from CH103 lineage. In certain embodiments the envelopes bind preferentially to an antibody or antibodies from CH235 lineage. In certain aspects the invention provides a polypeptide from the selections of envelopes listed in FIG. 14A (envelopes M5, M11, 20.14, 30.28, 30.23. and 136.B18), FIG. 15A (envelopes M5, M11, 20.14, 30.20, 30.23. and 136.B18), FIG. 16A (envelopes M5, M11, 20.14, 30.20, 30.12. and 136.B18), FIG. 18A (envelopes M5, M11, 20.14, 30.20, 30.12, and 136.B18), FIG. 20 (M5, 30.25; 53.25; and 53.29), FIG. 21 (M5, w30.20, w20.14, w30.12), or any combination thereof. In certain aspects the invention provides a composition comprising any suitable form of the nucleic acids of the invention. In certain aspects the invention provides a composition comprising any suitable polypeptide, wherein the polypeptide is engineered and recombinantly produced.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. To conform to the requirements for PCT patent applications, many of the figures presented herein are black and white representations of images originally created in color.

FIG. 1 shows sequences of six envelopes (SEQ ID NOS 19-67, respectively, in order of appearance): CH505.M5gp145, CH505.M11gp145, CH505w020.14gp145, CH505w030.28gp145, CH505w078.15gp145, CH505w053.31gp145, also as gp120D8 and gp160 amino acid and nucleic acid sequences.

FIG. 2A shows sequences of ten envelopes (SEQ ID NOS 68-98, respectively, in order of appearance): CH505.M5gp145, CH505.M11gp145, CH505w020.14gp145, CH505w030.28gp145, CH505w078.15gp145, CH505w53.16gp145, CH505w30.21gp145, CH505w78.33gp145, CH505w100.B6gp145, CH505w053.31gp145, amino acid and nucleic acid sequences.

FIG. 2B shows sequences of ten envelopes (SEQ ID NOS 99-124, respectively, in order of appearance): CH505.M5D8gp120, CH505.M11D8gp120, CH505w020.14D8gp120, CH505w030.28D8gp120, CH505w078.15D8gp120, CH505w053.16D8gp120, CH505w030.21D8gp120, CH505w078.33D8gp120, CH505w100.B6D8gp120, CH505w053.31D8gp120 as amino acids and nucleic acids.

FIG. 2C shows sequences of ten envelopes of FIG. 2B as gp160 amino acid and nucleic acid sequences (SEQ ID NOS 125-144, respectively, in order of appearance).

FIGS. 3A-C shows the genotype variation (A, left panel), neutralization titers (B, center panel), and Envelope phylogenetic relations (C, right panel) among CH505 Envelope variants. The vertical position in each panel corresponds to the same CH505 Env clone named on the right side of the tree. Distance from the Transmitted/Founder form generally increases from top towards bottom of the figure. In the left panel (A), sites not colored correspond to the Transmitted/Founder virus, thin boxed sites show mutations, and hashed boxed sites correspond to insertions or deletions relative to the Transmitted/Founder virus. Additional annotation indicates the known CD4 binding-site contacts (short, vertical black bars towards top), CH103 binding-site contacts for the resolved structure (short, vertical transparent bars with a horizontal line to indicate the region resolved by X-Ray Crystallography), gp120 landmarks (vertical boxed rectangular regions, V1-V5 hypervariable loops, Loop D, and CD4 Loops), a dashed vertical line delineating the gp120/gp41 boundary, and results from testing for CTL epitopes with ELISpot assays (lined rectangle at top and bottom show where peptides were tested and negative, and a wavy rectangle for the tested positive region outside the C-terminal end of V4). The center panel (B) depicts IC50 (50% inhibitory concentrations, in μg/ml) values from autologous neutralization assays against 13 monoclonal antibodies (MAbs) of the CH103 lineage and each of 134 CH505 Env-pseudotyped viruses. Hashing scale values indicate neutralization potency and range from speckled (no neutralization detected) through wide left-to-right diagonal hashed (potent neutralization, i.e. <0.2 μg/ml; empty cells correspond to absence of information). The cumulative progression of neutralization potency from left to right, corresponding to developmental stages in the CH103 lineage, indicates accumulation of neutralization potency. Similarly, increased presence neutralization signal from top to bottom corresponds to increasing neutralization breadth per MAb in the CH103 lineage. In the right-most panel (C) is the phylogeny of CH505 Envs, with the x-axis indicating distance from the Transmitted-Founder virus per the scale bar (units are mutations per site). The tree is ordered vertically such that lineages with the most descendants appear towards the bottom. Each leaf on the tree corresponds to a CH505 autologous Env, with the name of the sequence depicted (‘w’ and symbol hash pattern indicate the sample time-point; ‘M’ indicates a synthetic mutant Env). The hash pattern of the corresponding diamond(s) to the left of each leaf name indicates its inclusion in a possible embodiment, or no diamond for exclusion from any embodiments described herein. Three long, vertical lines to the left of the tree depict the phylogenetic distribution of envelopes in three distinct alternative embodiments (identified as “Vaccination Regimes 1-3”), with diamonds used to identify each.

FIGS. 4-8 show Heat Map of Binding (log Area Under the Curve, AUC) of Sequential Envs to CH103 and CH235 CD4 Binding Site Broadly Neutralizing Antibody Lineages members. Numerical data corresponding to the graphic representations in these figures are shown in Tables 2-5 in Example 2.

FIG. 9 shows neutralization activity of CH103 clonal lineage antibodies against autologous CH505 viruses.

FIG. 10 shows neutralization susceptibility of the CH505 loop D mutants to CH103 lineage antibodies.

FIG. 11 shows CH103 ELISA binding data and choice of immunogens.

FIG. 12 shows neutralization susceptibility of CH505 loop D mutants to CH235 lineage antibodies.

FIG. 13 shows neutralization activity of CH235 clonal lineage antibodies against autologous CH505 viruses.

FIGS. 14A-B show a heat map of binding log Area Under the Curve, AUC) of Sequential Envs M5, M11, 20.14, 30.28, 30.23, 136.B18 to CH103 (FIG. 14B) and CH235 (FIG. 14A-includes lineage member CH557) CD4 Binding Site Broadly Neutralizing Antibody Lineages members.

FIGS. 15A-B show a heat map of binding log Area Under the Curve, AUC) of Sequential Envs M5, M11, 20.14, 30.20, 30.23, 136.B18 to CH103 (FIG. 15B) and CH235 (FIG. 15A-includes lineage member CH557) CD4 Binding Site Broadly Neutralizing Antibody Lineages members. Env 30.20 has better progression for CH235 whereas 30.28 has better progression for CH103, however early CH103 intermediates are covered well by 20.14.

FIGS. 16A-B show a binding log Area Under the Curve, AUC) of Sequential Envs M5, M11, 20.14, 30.20, 30.12, 136.B18 to CH103 (FIG. 16B) and CH235 (FIG. 16A-includes lineage member CH557) CD4 Binding Site Broadly Neutralizing Antibody Lineages members.

FIGS. 17A-B show amino acid and nucleic acid sequences of M5, M11, 20.14, 30.20, 30.12, 136.B18 envelopes: FIG. 17A shows sequences of gp120D8 variants (SEQ ID NOS 145-156, respectively, in order of appearance), FIG. 17B shows sequences of gp160 envelopes (SEQ ID NOS 157-168, respectively, in order of appearance).

FIGS. 18A-B (see also FIGS. 52A-B from Example 8) show. CH505 gp120 Env Quasi-species Selected as Optimized Immunogens to Induce Both CH235 and CH103-like bnAbs, related to FIGS. 46A-B (Ex. 8). (A) Heatmap of the binding data of selected CH235 and CH103 lineage members to the CH505 Env glycoproteins selected to be used as immunogens. Individual Env clone names and weeks of isolation are shown on the left. (A) shows a binding log Area Under the Curve, AUC) of Sequential Envs M5, M11, 20.14, 30.20, 30.12, 136.B18 to CH235 (left panel) and CH103 (right panel) CD4 Binding Site Broadly Neutralizing Antibody Lineages members. (B) Affinity of gHgL of 1B2530, 8ANC131, VRC01, VRC-PG04 and VRC-CH31 to a panel of 15 heterologous gp120 envelope glycoproteins.

FIGS. 19A-B show nucleic acid and amino acid sequences of M5, M11, 20.14, 30.20, 30.12, 136.B18 envelopes (SEQ ID NOS 169-194, respectively, in order of appearance). The highlighted portions indicate non-coding sequences—one stop codon at the end of each nucleotide sequences is not highlighted.

FIG. 20 shows a selection for a Sequential Vaccine. Heat Map of Binding (log Area Under the Curve, AUC) of Sequential Envs to CH235 VH1-46 type of CD4 mimic, CD4 Binding Site Broadly Neutralizing Antibody Lineage Members for sequential immunization. X axis shows CH235 antibody lineage members, from UCA to mature antibodies, from left to right.

FIG. 21 shows a selection for a Sequential Vaccine. Heat Map of Binding (log Area Under the Curve, AUC) of Sequential Envs to CH235 VH1-46 type of CD4 mimic, CD4 Binding Site Broadly Neutralizing Antibody Lineage Members for sequential immunization.

FIG. 22A shows CH505 chimeric 6R.SOSIP.664 design. The gp120 of CH505 (right) except the c-terminal 37 amino acids was transplanted into the well-characterized A.BG505 6R.SOSIP.664 (left). The transplantation design takes advantage of the enhanced stability of the A.BG505 strain. The resultant chimeric molecule (center) has the CH505 gp120 (yellow) fused to the 37 c-terminal amino acids of A.BG505 (blue) and the A.BG505 gp41 (magenta).

FIG. 22B shows nucleic acid sequences of various trimer designs of FIG. 23A (SEQ ID NOS 195-233, respectively, in order of appearance).

FIG. 23A shows amino acid sequences of various trimer designs (SEQ ID NOS 234-272). In some embodiments the leader sequence for these proteins is MPMGSLQPLATLYLLGMLVASVLA (SEQ ID NO: 273).

FIG. 23B shows annotated sequence of SOSIP.III design (SEQ ID NOS 273-276, respectively, in order of appearance).

FIG. 24A shows amino acid and nucleic acid sequences of designs CH505TF.6R.SOSIP.664.v4.1_AMBRCTA and AMBRCTAG, and designs CH505M5chim.6R.SOSIP.664v4.1_AMBRCTA and AMBRCTAG (SEQ ID NOS 277-288, 290, 289, 292, 291, 294, 293, 295 and 296, respectively, in order of appearance). See also Example 9.

FIGS. 24B, C and D show sortase designs and nucleic acid and protein sequences (SEQ ID NOS 297-308, respectively, in order of appearance).

FIG. 24E shows the PGT151 antibody staining of 293F cells transiently transfected with AMBRCTA and AMBRCTAG constructs of FIG. 24A. Only the TM constructs show surface expression of Trimeric Envelope.

FIG. 24F shows the quantification of SOSIP trimer in the supernatant of cells transfected with the constructs of FIG. 24A

FIG. 24G shows ferritin designs (SEQ ID NOS 309-313, respectively, in order of appearance).

FIG. 24H shows antigenicity of M5 SOSIPv4.1 ferritin particle.

FIG. 24I shows comparison of binding of the M5 trimer alone versus the M5 trimer multimerized on the ferritin particle.

FIG. 24J shows negative stain EM of M5 trimers on the ferritin particle. The ring in the middle is ferritin and the trimer is the spikes coming off of the ring.

FIG. 25 shows design of rhesus macaque immunogenicity study. The immunization schedule is shown in this figure. The study compared the immunogenicity of the CD40 targeted Env to the wildtype Env in a rhesus macaque immunogneicity study. The macaques were immunized intramuscularly and electroporated twice with DNA encoding the CH505 T/F gp145. After DNA priming the macaques were administered sequential CH505 recombinant gp140C oligomers from the transmitted founder virus, and weeks 53, 78, and 100. Three macaques were immunized with the CH505 Envs conjugated to CD40 and 4 macaques were administered the CH505 Env as gp140C envelopes. We examined binding antibody titer by ELISA, neutralizing antibody titers by the TZM-bl assay, and profiled the antibody repertoire by monclonal antibody isolation. The study analyzed the immunogenicity of wildtype and CD40-targeted Env using antibody ELISA binding, TZM-bl neutralization assay, and will isolate monoclonal antibodies.

FIG. 26 shows plasma IgG responses to CH505 transmitted/founder gp140. This figure shows the binding titers over time with each symbol representing an individual macaque and the red line and symbol indicating the those animals that received the wildtype Env. The macaques that were immunized with the Env conjugated to anti-CD40 are shown in blue. The titers in both groups was comparable until week 18 which was 2 weeks after the second protein boost. After that boost with the week 53 Env the wildtype group tended to have higher binding antibody titers.

FIG. 27 shows CH505 gp140 vaccination induces plasma blocking of CD4 binding. The figure shows whether CD4 binding site antibodies were present in the plasma using competition ELISAs for soluble CD4 (shown on the left and a bnAb from the CH103 lineage called CH106 shown on the right. We examined the plasma blocking activity shown on the y-axis over time and found that at week 18 the CD4 binding site response was dramatically reduced to near background levels in the CD40 IgG4—Env group compared to the wildtype Env which showed 70 and 80% blocking of soluble CD4 and CH106 respectively.

FIG. 28 shows that plasma IgG exhibits CD4 binding site-directed binding to a resurfaced gp120 core. This figure shows the ability of the plasma IgG from all four animals to bind to RSC3 or its CD4 knock out mutant. Shown here is the difference in binding between the wildtype RSC3 and the CD4 binding site mutant over time.

FIG. 29 shows CH505 gp140 vaccination elicits high titers of autologous tier 1 virus neutralization. This figure shows the neutralization titers for each macaque represented as ID50 reciprocal dilutions against a tier 1 virus called CH505 w4.3 isolated from the CH505 individual early in infection. All 4 animals generated relatively high titers of tier 1 neutralizaing antibodies beginning with the protein boost. The titers were increased with subsequent boosts with the sequential vaccine, and notably these tier 1 neutralizing antibodies were typical for our CH505 Env vaccinations that have been performed in macaques.

FIG. 30 shows CH505 gp140 sequential vaccination boosts autologous tier 2 CH505 TF virus neutralization. This figure shows autologous tier 2 neutralization by the plasma from each macaque. The ID50 titers are shown for each macaque and we observed 1 of 4 macaques generated autologous tier 2 neutralizing antibodies in the plasma. Detectable neutralization first occurred after the CH505 week 53 Env protein boost and increased with each boost. This result was striking since this macaque was the first vaccinated macaque where we observed neutralization of the CH505 TF virus.

FIG. 31 shows autologous neutralizing antibodies against all four tier 2 viruses increased with sequential boosting. This figure shows the autologous tier 2 neutralization analysis to include the tier 2 CH505 viruses that comprise the sequential vaccination regimen. The same macaque 6207 was able to neutralize all four tier 2 CH505 viruses. The neutralization was detectable against 3 of 4 of the CH505 viruses after only 2 protein boosts, and by three boosts all 4 viruses were neutralized. We saw the neutralizing titers continued to increase with each boost.

FIG. 32 shows NHP 6207 neutralizes heterologous tier 2 virus representative global isolates. While autologous tier 2 neutralization is difficult to elicit, heterologous tier 2 neutralization is even more rare to observe in vaccinated primates. To determine whether tier 2 heterologous breadth was elicited in macaque 6207 plasma we tested neutralization against heterologous tier 2 viruses selected to represent the global circulating viruses. We examined neutralization of this 12 virus panel by the plasma at week 30-post 4 sequential protein boosts and week 36 post 5 sequential protein boosts. After 4 protein boosts two heterologous tier 2 viruses were neutralized. After the subsequent boost 9/12 of the viruses were neutralized. Although the titers were low this antibody response appears boostable and is currently the broadest tier 2 neutralization known to be achieved in a vaccinated primate.

FIG. 33 shows B cell sorting for CD4 binding site differential antibodies. Memory B cells from two macaques were sorted and compared the presence of RSC3-reactive B cells that did not bind the CD4 knock out mutant version of the protein called delta RSC3. A representative FACS plot is shown on the left for the NHP 6207 who possessed SCL70 reactive plasma IgG and developed broadly neutralizing antibodies in its plasma. For comparison we sorted RSC3-reactive B cells from NHP 6436, which did not have broad neutralization in the plasma but was the other macaque that tested positive for auto antibodies. The NHP 6207 had a relatively large percentage of RSC3 reactive B cells whereas NHP6436 had very few.

FIG. 34 shows macaque 6207 has broad plasma neutralization and antibodies against Scl70. This figure shows autoreactivity measured in the Athena assay for each of the four macaques that received the wildtype CH505 gp140C envelopes in vaccination. Median fluorescence intensity for binding to each autoantigen listed on the x-axis is depicted in separate graphs for each macaque. The positivity threshold for the assay is marked by the dotted line. Interestingly, the macaque that possessed broad neutralization possessed binding antibodies to the autoantigen SCL70, which is correlated of the autoimmune disease scleroderma. The antibodies were present prior to vaccination indicated by the binding in the grey bar. One other macaque tested positive for autoantibodies, but it bound to a different autoantigen.

FIG. 35 shows a heterologous panel heatmap of IC50s.

FIG. 36 shows the global panel, grouped by bNAb sensitivity (right panel). Env mutations over time in subject CH505, by week is shown in the left panel.

FIG. 37 shows V5 selection yields population breadth.

FIG. 38 shows mutations and V5 length.

FIG. 39 shows a selection of four envelopes from CH505 and their binding to CH235 lineage antibodies.

FIG. 40 shows a selection of CH505 immunogens to drive both CH103 and CH235 CD4 binding site types of broad neutralizing B cell lineages.

FIGS. 41A-B show CH235 Lineage, with Time of Appearance and Neutralization by Select Members. (A) Phylogram of CH235 lineage. Phylogenetic tree is colored by first time (wk post-infection) from which sequences were obtained. Key members of the CH235 lineage are labeled. CH235.6, CH235.7, CH235.8 and CH235.9 V_(H) were complemented with full heavy chain gene regions and paired with the V_(L) from the closest natural antibody. (B) Neutralization dendrograms display single mAb neutralization of a genetically diverse panel of 199 HIV-1 isolates. Coloration is by IC₅₀. See also FIGS. 48A-B, 53, and 54.

FIGS. 42A-E show structures of CH235-Lineage Members in Complex with HIV-1 Env. (A) Co-crystal structures of the antigen-binding fragments (Fabs) of CH235-lineage members with core gp120. Structures are shown in ribbon diagram, with gp120 in gray and residues altered by SHM in stick representation colored by time-of-appearance. (B) Negative stain EM of Fabs of CH235-lineage members and trimeric HIV-1 Env from BG505 (top row) and B41 (bottom row). Structures in surface representation, with Env portions colored gray and Fabs by time-of-appearance. (C) Epitope displayed on the gp120 surface and colored by antibody time-of-appearance, with the vulnerable portion of the CD4bs highlighted in yellow and select regions labeled. (D) Targeting precision of CD4bs-directed antibodies vs neutralization breadth. (E) V_(H)-gene SHM of CD4bs-directed antibodies vs neutralization breadth. See also FIGS. 49A-G and FIG. 55.

FIG. 43A-C shows sequence Evolution of CH235 Lineage: SHM, Timing, and Conformity of CH235-Lineage Development from UCA to Antibody with 90% Breadth. (A) Heavy chain SHM over time for the CH235 lineage (left panel). SHM levels of other V_(H)1-46-derived CD4bs mAbs and selected V_(H)1-2-derived VRC01-class mAbs are shown (middle and right panels, respectively); the time since infection is unknown for these mAbs. (B) Maturation conformity vs overall heavy chain SHM. Positional conformity (top row) is defined as the number of aa positions differing from the germline sequence in both the conforming and reference sequences, divided by the total number of aa changes in the conforming antibody. Identity conformity (bottom row) is defined as the number of such positions which are additionally mutated to the same residue, divided by the total number of mutations in the conforming antibody. Conformity to 1B2530 (left) and to 8ANC131 (right) is shown for both position and identity. (C) V_(H)-gene mutability accounts for the majority of positional conformity of CH235 lineage. The mutability of the V_(H)-gene for V_(H)1-46 (top) and V_(H)1-2 (bottom) is shown. Sequence logos are shown at each position; the height of each logo corresponds to the percent of mutated reads. Green bars are shown for SHM in antibody CH235, which are altered in over a quarter of V_(H)1-46-derived antibodies. See also FIGS. 50A-E and 56A-C. FIG. 43C discloses SEQ ID NOS 314-323, respectively, in order of appearance.

FIGS. 44A-D show binding Kinetics of CH103 and CH235 Lineage Antibodies. Binding association (k_(a)) and dissociation (k_(d)) rates of the CH103 (A-B, squares) and CH235 (C-D, circles) lineage mAbs to CH505.TF gp120 Env were measured with SPR and used to calculate the dissociation rate constants (K_(d)). K_(d)s are shown in A and C, k_(a) (solid lines, plotted on the left y-axis) and k_(d) (dashed lines, plotted on the right y-axis) are shown in B and D. See also FIGS. 57A-B.

FIGS. 45A-C show CH235 Lineage Antibodies Neutralization of Autologous Virus and CH505.TF Loop D Mutants. (A) Heatmap analysis of neutralization of 76 pseudoviruses (row) by 16 CH235 lineage mAbs (column). Coloration is by IC₅₀. This analysis extends previous observations on early CH235 lineage antibodies (Gao et al., 2014) by including late mAbs CH235.7, CH235.8, CH235.10, CH235.11, CH235.12 and CH235.13 and by adding pseudoviruses isolated from wk 136 to 323 post-transmission. (B) CH505 TF and loop D mutants M5, M6, M10, M19, M11, M7, M8, M9, M20 and M21 neutralization by CH236 mAb, late mAbs CH235.7, CH235.9 CH235.10, CH235.11, CH235.12, CH235.13 (left panel) and CH235.9 mAb mutants (right panel). Neutralization is expressed as IC₅₀ μg/ml. CH505 TF sequence mutations are shown on the right. (C) The CDR H1 N30 (sticks, dark red) in CH235.9, which interacts with the β20-β21 loop in the bridging sheet of gp120 (cyan), is over 19 Å away from the N280S mutation site in loop D (orange). See also FIGS. 51A-B, 58, and 59.

FIGS. 46A-B show binding of CH235 and CH103 Lineage mAbs to Autologous CH505 (A) and CH235 UCA Binding to Heterologous HIV-1 Env Glycoproteins (B). (A) Heatmap analysis of UCA, intermediate (IA) and mature CH235 and CH103 lineage mAbs binding to 113 CH505 autologous Env isolated from time of infection (TF) to 160 wks post-infection and to the CH505.TF mutants (Gao et al., Cell 2014). Mabs were tested in ELISA at concentrations ranging from 100 μg/ml to 0.6 ng/ml. Binding is expressed as a LogAUC. (B) Affinity of CH235 UCA, CH235 wild-type and select SHM variants to a panel of 15 heterologous gp120 Envs. See also FIGS. 52A-B and 60.

FIGS. 47A-D show CH235 Antibody Lineage Auto- and Polyreactivity. (A) CH235 lineage antibody binding to ANA measured in ELISA. LogAUC was calculated from duplicate samples. Results representative of duplicate experiments. (B) Binding to cardiolipin was determined using Quanta Lite ACA IgG III ELISA Assay. (C) Hep2 cell IF staining. Size bars=50 μm. (D) Measurement of polyreactivity against 9,400 human antigens using ProtoArray 5 microchip: CH235 lineage mAbs binding (x-axis) was compared to non-polyreactive control mAb 151K (y-axis). Polyreactivity is defined as 1 log stronger binding than 151 k mAb to more than 90% of the test proteins. High affinity binding was measured as a >2 log increase in binding (dotted line) (Liu et al., 2015).

FIGS. 48A-B show CH235 Lineage: Sequences and Neutralization Fingerprint Dendrogram, related to FIGS. 41A-B. (A) Alignment of NGS sequences (SEQ ID NOS 324-385, respectively, in order of appearance) and antibodies isolated from 17 time points from 6 to 323 weeks post-transmission and comparison of mutation patterns to other IGHV1-46 (1B2530 and 8ANC131) and IGHV1-2 (VRC01, VRC-CH31 and VRC-PG04) derived broadly neutralizing antibodies. Antibodies isolated from single B cells are shown in bold. The positions mutated in CH235 were color coded based on the time points at which these mutations were firstly observed in the NGS reads. Mutated positions not seen in the NGS data are colored based on the time of isolation of CH235 (41 weeks). IGHV1-46*01 is used as reference for IGHV1-46 derived antibodies and IGHV1-2*02 is used as reference for the three VRC01-class antibodies. (B) The neutralization fingerprints for three antibodies from the CH235 lineage were compared to the fingerprints for other VH1-46 class antibodies and non-VH1-46 class CD4-binding-site antibodies; coloring same as in FIGS. 43A-C. Antibodies targeting other sites of vulnerability on HIV-1 Env are shown as control (black).

FIGS. 49A-G show CH235 Lineage Versus Other CD4-Binding Site Antibodies and Negative-stain EM Reconstructions of gp140 SOSIP Trimers with CH235-lineage Fabs, related to FIGS. 42A-E. (A) CD4-mimicry by CH235. Recognition of gp120 by the N-terminal domain of the CD4 receptor (far left) is compared to VH genes from CH235 and prototypic antibodies VRC01 (from VH1-2) and 8ANC131 (from VH1-46). (B) Conserved molecular interactions between antibody CH235, receptor CD4 and antibody VRC01. Top row shows intermolecular antiparallel strand interactions and bottom row Asp368 electrostatic interaction. (C) Binding orientation of VH-gene derived antibodies relative to CD4. (D) Negative-stain EM 3D models with BG505 SOSIP.664. (left) Top and side views of CH235.12 in complex with BG505 SOSIP (purple) aligned to the EM volume of VRC01 in complex with BG505 (gold mesh; EMD-6252). (middle) Top and side views of the CH235.12-BG505 complex (purple mesh) aligned to the EM volume of CH103 in complex with BG505 SOSIP (gray; EMD-6250). (right) Top and side views of the CH103-BG505 complex (gray mesh) aligned to the EM reconstruction of BG505 SOSIP in complex with soluble CD4 and 17b Fab (blue; EMDB ID 5723). (E) Negative-stain EM of gp140 SOSIP trimers with CH235-lineage Fabs. (F) Top and side views of 3D reconstructions of each complex. (G) Fourier shell correlation curves for each dataset with a resolution estimate using an FSC cutoff of 0.5.

FIGS. 50A-E shows sequence Similarity Between VH1-2 and VH1-46 Broadly Neutralizing Antibodies and Mutability of Germline Genes, related to FIGS. 43A-C. (A) Amino acid alignment of 8ANC131 (SEQ ID NO: 387) and CH235 (SEQ ID NO: 388) to the IGHV1-46 (SEQ ID NO: 386) germline gene showing the definition of conformity. (B) Probability distribution of the number of sharing mutation positions for each pair of antibodies. (C) Probability distribution of the number of identical mutations for each pair of antibodies. (D) SHM frequency is shown versus VH-gene position for VH1-46, VH1-2 and three others. Sequences were aligned to VH1-46 and positions not aligned to VH1-46 (indels) were removed. (E) Dendrogram showing sequence segregation of VH1-2 and VH1-46 derived broadly neutralizing antibodies, despite similarity of VH1-2 and VH1-46 germline genes shown with underline.

FIGS. 51A-B shows generation of CH235.9 Mutants to Evaluate the Effect of Mutations in the V-heavy Chain on the Ability of CH235.9 to Neutralize loop D Mutant CH505 Autologous Viruses, related to FIGS. 45A-C. (A) The interaction between CH235 CDR L3 (purple) and N280 in the HIV-1 gp120 Env loop D (orange) from the crystal structure of the CH235-gp120 complex (left panel). Asparagine in position 280 in gp120 forms three hydrogen bonds (yellow dotted lines) with residues in the CDR L3 (left panel). Structural modeling predicted these hydrogen bonds to be disrupted in the N280S (right panel) and N280T (not shown) mutations which occur in autologous CH505 escape mutants. (B) Alignment of CH235.7 and CH235.9 through CH235.13 VH amino acid sequences to CH236 VH. CH235.9 aa mutations expressed as recombinant IgG and tested for neutralization of CH505 TF loop D mutants are shown in red (SEQ ID NOS 389-395, respectively, in order of appearance). Asterisks indicate points of contact with gp120 derived from the CH235 crystal structure in complex with gp120 Env.

FIGS. 52A-B show CH505 gp120 Env Quasi-species Selected as Optimized Immunogens to Induce Both CH235 and CH103-like bnAbs, related to FIGS. 46A-B. (A) Heatmap of the binding data of selected CH235 and CH103 lineage members to the CH505 Env glycoproteins selected to be used as immunogens. Individual Env clone names and weeks of isolation are shown on the left. (B) Affinity of gHgL of 1B2530, 8ANC131, VRC01, VRC-PG04 and VRC-CH31 to a panel of 15 heterologous gp120 envelope glycoproteins.

FIG. 53 shows characteristics of the V(D)J rearrangements of key CH235 lineage antibodies. Related to FIGS. 41A-B.

FIG. 54 shows a summary of the Breadth and Potency of Antibody Neutralization Against 199 HIV-1 Env-Pseudoviruses. Related to FIGS. 41A-B.

FIG. 55 shows Crystallographic Data Collection and Refinement Statistics. Related to FIGS. 42A-E.

FIGS. 56A-C show sequence Similarity Between VH1-2 and VH1-46 Broadly Neutralizing Antibodies and Mutability of Germline Genes. Related to FIGS. 43A-C. (A) The probability of a conforming VH1-46 antibody with x V_(H) mutations, having c common mutation positions with a reference antibody were estimated based on 100,000 simulated events, with the likelihood of each residue being mutated based on uniform distribution (position) (P_(uniform)), or the mutation frequency at each residue position derived from the VH1-46 antibodies (P_(VH1-46)). (B) The probability of a conforming VH1-46 antibody with x V_(H) mutations, having i identical mutations with a reference antibody were estimated based on 100,000 simulated events, with the likelihood of each residue being mutated based on uniform distribution (position and mutation type) (P_(uniform)), or the mutation frequency at each residue position derived from the VH1-46 antibodies (P_(VH1-46)). (C) Pearson correlation coefficients of positional somatic mutation frequency between VH1-46, VH1-2 and three others.

FIGS. 57A-B show CH235 Lineage and CH106 Monoclonal Antibodies Cross-Blocking. Related to FIGS. 44A-D. (A) CH235 lineage antibodies blocking of sCD4 and CH106 binding to CH505 TF gp120 and B.63521 gp120 Envs. Results expressed as IC50 ug/ml. nb=no blocking. (B) Monoclonal antibody CH106 blocking of CH235 lineage antibodies to CH505 TF gp120. Results expressed as IC50 ug/ml. nb=no blocking.

FIG. 58 shows CH235 lineage autologous neutralization. Related to FIGS. 45A-C.

FIG. 59 shows CH235 lineage antibodies and CH235.9 mutants neutralization of CH505 TF loop D mutant viruses. Related to FIGS. 45A-C.

FIG. 60 shows binding of antibodies in the CH235 and CH103 lineages to CH505 autologous Env glycoproteins, Related to FIGS. 46A-B.

FIG. 61 shows stabilization of chimeric CH505 TF SOSIP gp140. The introduction of a cysteine at positions 201 and 433 formed a disulfide bond that stabilized the trimer in the pre-CD4 bound conformation (Nat Struct Mol Biol. 2015 July; 22(7): 522-531). This mutation was also added to further stabilize the CH505 chimeric SOSIP.

FIG. 62 shows CH505 SOSIP.I binds to trimer-specific bnAbs. The chimeric CH505 TF SOSIP.I was produced and tested for binding to trimer specific bnAbs. In SPR assays, CH505 bound both PGT145 and PGT151.

FIG. 63 shows SOSIP.I—stabilization of the trimer to reduce CD4 binding also disrupts binding by the CH103 lineage. When the UCA of the CH103 lineage or a mature bnAb from the lineage CH106 was assessed for binding to the CH505 TF SOSIP.I neither antibody bound to the trimer. In contrast the CD4 mimicking antibody VRC01 was still able to bind.

FIG. 64 shows CH103 UCA binds the CH505 transmitted founder gp120. The monomeric CH505 TF gp120 binds to the CH103 UCA by SPR as shown in the box.

FIG. 65 shows CH505 TF SOSIP.II—removal of the DS mutations to improve CD4bs Ab binding. To test whether the DS stabilizing mutations disrupted CH103 UCA binding, since they were reported to decrease CD4 binding, the cysteine mutations were reverted back to the alanine and isoleucine present in the wildtype virus. The antigenicity of these trimers, called SOSIP.II, was tested.

FIG. 66 shows removal of the disulfide stabilizing bond improves UCA binding. A summary of the binding of first SOSIP design called SOSIP.I for comparison to the SOSIP.II proteins is shown. The binding is heat mapped where the darker the color the stronger the binding in BLI experiments. Identical to the first SOSIP design, PGT151 and PGT145 bound to the SOSIP.II design relatively strongly indicating trimer formation. The CH103 lineage antibodies were also able to in bind the SOSIP.II version of the chimeric CH505 trimer. This design still had the V3 loop exposed and at least a portion of the trimers were in a CD4 bound conformation as indicated by 19B and 17B binding.

FIG. 67 shows CH505 TF chimeric SOSIP.III—introduction of two stabilizing mutation to reduce V3 exposure. Two mutations that reduced V3 exposure in nonchimeric SOSIPs were tested to see if these mutations could function similarly in the chimeric SOSIP design.

FIG. 68 shows CH505 TF chimeric SOSIP.III forms trimeric envelope and binds the CH103 UCA. The two mutations were introduced and the ability of this protein to form trimers was assessed by PGT151 binding and by negative stain EM. As shown on the left this protein bound to the trimer specific bnAb PGT151, and the protein formed a trimer as shown in the negative stain EM on the right.

FIG. 69 shows CH103 UCA binds to the CH505 TF SOSIP.III. When binding of the SOSIP.III was assessed and compared to the CH505 TF gp120, it was observed that the off-rate for the CH103 UCA was 10-fold better for the trimer which resulted in an approved affinity for the timer compared to the gp120.

FIG. 70 shows affinity maturation to the TF SOSIPv4.1 correlates with neutralization potency. The binding of the members of the CH103 lineage to the CCH505 TF was assessed. A positive correlation between affinity for the CH505 TF SOSIP.III was found, shown here on the y-axis and bottom row of the table and neutralization potency against the CH505 TF virus shown here on the x-axis and in the table. As antibodies affinity matured and could bind more strongly to the CH505 TF trimer, they also were able to neutralize the CH505 virus more potently.

FIG. 71 shows the CH103 mature bnAb engages each protomer of the CH505 TF SOSIP.III. The high affinity of the CH103 mature antibodies for these trimers provided an opportunity to study the stoichiometry of the interaction of the bnAb CH103 and its autologous Envelope. The unliganded trimer formed trimers and upon incubating it with CH103 Fab three CH103 Fabs were observed indicated by the arrows bound to each trimer. Thus the CH103 and gp140 had a 1 to 1 ratio for binding.

FIG. 72 shows rational design to improve the antigenicity of CH505 TF trimers. The SOSIP.III had the desired antigenicity for the CH103 lineage of antibodies. Its antigenicity on a larger panel of bnAbs was assessed. It bound to bnAbs but unlike the SOSIP.II it did not bind to 19B or 17B.

FIG. 73 shows CH505 Envs from sequential viruses form stable trimers as chimeric SOSIP.II and III.

This approach has been employed to multiple CH505 Env sequences in order to make sequential vaccination regimens. A 4-valent vaccination regimen of SOSIP.II was made. The same 4-valent vaccine was made using the SOSIP.III design. A 6-valent vaccine can be made. Trimers to were analyzed for glycosylation and disulfide bond analysis and the Envs have the expected glycosylation and lack aberrant disulfide bonds.

FIG. 74 shows the chimeric SOSIP.III design is applicable to diverse viruses. This design can be extrapolated to Envs that are not from the CH505 infected individual. Envs from clade C or AE or a group M consensus have all been used and form stable trimers using this design. This highlights the general applicability of this trimer design.

DETAILED DESCRIPTION OF THE INVENTION

The development of a safe, highly efficacious prophylactic HIV-1 vaccine is of paramount importance for the control and prevention of HIV-1 infection. A major goal of HIV-1 vaccine development is the induction of broadly neutralizing antibodies (bnAbs) (Immunol. Rev. 254: 225-244, 2013). BnAbs are protective in rhesus macaques against SHIV challenge, but as yet, are not induced by current vaccines.

For the past 25 years, the HIV vaccine development field has used single or prime boost heterologous Envs as immunogens, but to date has not found a regimen to induce high levels of bnAbs.

Recently, a new paradigm for design of strategies for induction of broadly neutralizing antibodies was introduced, that of B cell lineage immunogen design (Nature Biotech. 30: 423, 2012) in which the induction of bnAb lineages is recreated. It was recently demonstrated the power of mapping the co-evolution of bnAbs and founder virus for elucidating the Env evolution pathways that lead to bnAb induction (Nature 496: 469, 2013). From this type of work has come the hypothesis that bnAb induction will require a selection of antigens to recreate the “swarms” of sequentially evolved viruses that occur in the setting of bnAb generation in vivo in HIV infection (Nature 496: 469, 2013).

A critical question is why the CH505 immunogens are better than other immunogens. This rationale comes from three recent observations. First, a series of immunizations of single putatively “optimized” or “native” trimers when used as an immunogen have not induced bnAbs as single immunogens. Second, in all the chronically infected individuals who do develop bnAbs, they develop them in plasma after ˜2 years. When these individuals have been studied at the time soon after transmission, they do not make bnAbs immediately. Third, now that individual's virus and bnAb co-evolution has been mapped from the time of transmission to the development of bnAbs, the identification of the specific Envs that lead to bnAb development have been identified-thus taking the guess work out of envelope choice.

Two other considerations are important. The first is that for the CH103 bnAb CD4 binding site lineage, the VH4-59 and Vλ3-1 genes are common as are the VDJ, VJ recombinations of the lineage (Liao, Nature 496: 469, 2013). In addition, the bnAb sites are so unusual, we are finding that the same VH and VL usage is recurring in multiple individuals. Thus, we can expect the CH505 Envs to induce CD4 binding site antibodies in many different individuals.

Regarding the choice of gp120 vs. gp160, for the genetic immunization we would normally not even consider not using gp160. However, in acute infection, gp41 non-neutralizing antibodies are dominant and overwhelm gp120 responses (Tomaras, G et al. J. Virol. 82: 12449, 2008; Liao, H X et al. JEM 208: 2237, 2011). Recently we have found that the HVTN 505 DNA prime, rAd5 vaccine trial that utilized gp140 as an immunogen, also had the dominant response of non-neutralizing gp41 antibodies. Thus, we will evaluate early on the use of gp160 vs gp120 for gp41 dominance.

In certain aspects the invention provides a strategy for induction of bnAbs is to select and develop immunogens and combinations designed to recreate the antigenic evolution of Envs that occur when bnAbs do develop in the context of infection.

That broadly neutralizing antibodies (bnAbs) occur in nearly all sera from chronically infected HIV-1 subjects suggests anyone can develop some bnAb response if exposed to immunogens via vaccination. Working back from mature bnAbs through intermediates enabled understanding their development from the unmutated ancestor, and showed that antigenic diversity preceded the development of population breadth. See Liao et al. (2013) Nature 496, 469-476. In this study, an individual “CH505” was followed from HIV-1 transmission to development of broadly neutralizing antibodies. This individual developed antibodies targeted to CD4 binding site on gp120. In this individual the virus was sequenced over time, and broadly neutralizing antibody clonal lineage (“CH103”) was isolated by antigen-specific B cell sorts, memory B cell culture, and amplified by VH/VL next generation pyrosequencing. The CH103 lineage began by binding the T/F virus, autologous neutralization evolved through somatic mutation and affinity maturation, escape from neutralization drove rapid (clearly by 20 weeks) accumulation of variation in the epitope, antibody breadth followed this viral diversification.

Further analysis of envelopes and antibodies from the CH505 individual indicated that a non-CH103 Lineage (DH235) participates in driving CH103-BnAb induction. See Gao et al. (2014) Cell 158:481-491. For example V1 loop, V5 loop and CD4 binding site loop mutations escape from CH103 and are driven by CH103 lineage. Loop D mutations enhanced neutralization by CH103 lineage and are driven by another lineage. Transmitted/founder Env, or another early envelope for example W004.26, triggers naïve B cell with CH103 Unmutated Common Ancestor (UCA) which develop in to intermediate antibodies. Transmitted/founder Env, or another early envelope for example W004.26, also triggers non-CH103 autologous neutralizing Abs that drive loop D mutations in Env that have enhanced binding to intermediate and mature CH103 antibodies and drive remainder of the lineage. In certain embodiments, the inventive composition and methods also comprise loop D mutant envelopes (e.g. but not limited to M10, M11, M19, M20, M21, M5, M6, M7, M8, M9) as immunogens. In certain embodiments, the D-loop mutants are included in an inventive composition used to induce an immune response in a subject. In certain embodiments, the D-loop mutants are included in a composition used as a prime.

The invention provides various methods to choose a subset of viral variants, including but not limited to envelopes, to investigate the role of antigenic diversity in serial samples. In other aspects, the invention provides compositions comprising viral variants, for example but not limited to envelopes, selected based on various criteria as described herein to be used as immunogens. In some embodiments, the immunogens are selected based on the envelope binding to the UCA, and/or intermediate antibodies. In some embodiments the immunogens are selected based on their chronological appearance and/or sequence diversity during infection.

In other aspects, the invention provides immunization strategies using the selections of immunogens to induce cross-reactive neutralizing antibodies. In certain aspects, the immunization strategies as described herein are referred to as “swarm” immunizations to reflect that multiple envelopes are used to induce immune responses. The multiple envelopes in a swarm could be combined in various immunization protocols of priming and boosting. Immune responses, including B cell and T cell responses, could be measured by any suitable assay and criteria, such as but non limited plasma neutralization, plasma binding to vaccine and/or heterologous envelopes and/or viruses could be measured.

In certain embodiments the invention provides that sites losing the ancestral, transmitted-founder (T/F) state are most likely under positive selection. From acute, homogenous infections with 3-5 years of follow-up, identified herein are sites of interest among plasma single genome analysis (SGA) Envs by comparing the proportion of sequences per time-point in the T/F state with a threshold, typically 5%. Sites with T/F frequencies below threshold are putative escapes. We then selected clones with representative escape mutations. Where more information was available, such as tree-corrected neutralization signatures and antibody contacts from co-crystal structure, additional sites of interest were considered.

Co-evolution of a broadly neutralizing HIV-1 antibody (CH103) and founder virus was previously reported in African donor (CH505). See Liao et al. (2013) Nature 496, 469-476. In CH505, which had an early antibody that bound autologous T/F virus, we studied 398 envs from 14 time-points over three years (median per sample: 25, range: 18-53). We found 36 sites with T/F frequencies under 20% in any sample. Neutralization and structure data identified 28 and 22 interesting sites, respectively. Together, six gp41 and 53 gp120 sites were identified, plus six V1 or V5 insertions not in HXB2.

The invention provides an approach to select reagents for neutralization assays and subsequently investigate affinity maturation, autologous neutralization, and the transition to heterologous neutralization and breadth. Given the sustained coevolution of immunity and escape this antigen selection based on antibody and antigen coevolution has specific implications for selection of immunogens for vaccine design.

In one embodiment, five envelopes were selected that represent envelope antigenic diversity. In another embodiment, six envelopes were selected that represent envelope antigenic diversity. In another embodiment, ten envelopes were selected that represent envelope antigenic diversity. These sets of envelopes represent antigenic diversity by deliberate inclusion of polymorphisms that result from immune selection by neutralizing antibodies. These selections represent various levels of antigenic diversity in the HIV-1 envelope. In some embodiments the selections are based on the genetic diversity of longitudinally sampled SGA envelopes. In some embodiments the selections are based on antigenic and or neutralization diversity. In some embodiments the selections are based on the genetic diversity of longitudinally sampled SGA envelopes, and correlated with other factors such as antigenic/neutralization diversity, and antibody coevolution.

Sequences/Clones

Described herein are nucleic and amino acids sequences of HIV-1 envelopes. The sequences for use as immunogens are in any suitable form. In certain embodiments, the described HIV-1 envelope sequences are gp160s. In certain embodiments, the described HIV-1 envelope sequences are gp120s. Other sequences, for example but not limited to stable SOSIP trimer designs, gp145s, gp140s, both cleaved and uncleaved, gp140 Envs with the deletion of the cleavage (C) site, fusion (F) and immunodominant (I) region in gp41—named as gp140ΔCFI (gp140CFI), gp140 Envs with the deletion of only the cleavage (C) site and fusion (F) domain—named as gp140ΔCF (gp140CF), gp140 Envs with the deletion of only the cleavage (C)—named gp140AC (gp140C) (See e.g. Liao et al. Virology 2006, 353, 268-282), gp150s, gp41s, which are readily derived from the nucleic acid and amino acid gp160 sequences. In certain embodiments the nucleic acid sequences are codon optimized for optimal expression in a host cell, for example a mammalian cell, a rBCG cell or any other suitable expression system.

An HIV-1 envelope has various structurally defined fragments/forms: gp160; gp140—including cleaved gp140 and uncleaved gp140 (gp140C), gp140CF, or gp140CFI; gp120 and gp41. A skilled artisan appreciates that these fragments/forms are defined not necessarily by their crystal structure, but by their design and bounds within the full length of the gp160 envelope. While the specific consecutive amino acid sequences of envelopes from different strains are different, the bounds and design of these forms are well known and characterized in the art.

For example, it is well known in the art that during its transport to the cell surface, the gp160 polypeptide is processed and proteolytically cleaved to gp120 and gp41 proteins. Cleavages of gp160 to gp120 and gp41 occurs at a conserved cleavage site “REKR.” (SEQ ID NO: 1) See Chakrabarti et al. Journal of Virology vol. 76, pp. 5357-5368 (2002) see for example FIG. 1, and Second paragraph in the Introduction on p. 5357; Binley et al. Journal of Virology vol. 76, pp. 2606-2616 (2002) for example at Abstract; Gao et al. Journal of Virology vol. 79, pp. 1154-1163 (2005); Liao et al. Virology vol. 353(2): 268-282 (2006).

The role of the furin cleavage site was well understood both in terms of improving cleave efficiency, see Binley et al. supra, and eliminating cleavage, see Bosch and Pawlita, Virology 64 (5):2337-2344 (1990); Guo et al. Virology 174: 217-224 (1990); McCune et al. Cell 53:55-67 (1988); Liao et al. J Virol. April; 87(8):4185-201 (2013).

Likewise, the design of gp140 envelope forms is also well known in the art, along with the various specific changes which give rise to the gp140C (uncleaved envelope), gp140CF and gp140CFI forms. Envelope gp140 forms are designed by introducing a stop codon within the gp41 sequence. See Chakrabarti et al. at FIG. 1.

Envelope gp140C refers to a gp140 HIV-1 envelope design with a functional deletion of the cleavage (C) site, so that the gp140 envelope is not cleaved at the furin cleavage site. The specification describes cleaved and uncleaved forms, and various furin cleavage site modifications that prevent envelope cleavage are known in the art. In some embodiments of the gp140C form, two of the R residues in and near the furin cleavage site are changed to E, e.g., RRVVEREKR (SEQ ID NO: 2) is changed to ERVVEREKE (SEQ ID NO: 3), and is one example of an uncleaved gp140 form. Another example is the gp140C form which has the REKR site (SEQ ID NO: 1) changed to SEKS (SEQ ID NO: 4). See supra for references.

Envelope gp140CF refers to a gp140 HIV-1 envelope design with a deletion of the cleavage (C) site and fusion (F) region. Envelope gp140CFI refers to a gp140 HIV-1 envelope design with a deletion of the cleavage (C) site, fusion (F) and immunodominant (I) region in gp41. See Chakrabarti et al. Journal of Virology vol. 76, pp. 5357-5368 (2002) see for example FIG. 1, and Second paragraph in the Introduction on p. 5357; Binley et al. Journal of Virology vol. 76, pp. 2606-2616 (2002) for example at Abstract; Gao et al. Journal of Virology vol. 79, pp. 1154-1163 (2005); Liao et al. Virology vol. 353(2): 268-282 (2006).

In certain embodiments, the envelope design in accordance with the present invention involves deletion of residues (e.g., 5-11, 5, 6, 7, 8, 9, 10, or 11 amino acids) at the N-terminus. For delta N-terminal design, amino acid residues ranging from 4 residues or even fewer to 14 residues or even more are deleted. These residues are between the maturation (signal peptide, usually ending with CX, X can be any amino acid) and “VPVXXXX . . . ”. In case of CH505 T/F Env as an example, 8 amino acids (italicized and underlined in the below sequence) were deleted:

(SEQ ID NO: 5) MRVMGIQRNYPQWWIWSMLGFWMLMICNG MWVTVYYG VPVWKEAKTTLFC ASDAKAYEKEVHNVWATHACVPTDPNPQE . . . (rest of envelope sequence is indicated as “. . .”). In other embodiments, the delta N-design described for CH505 T/F envelope can be used to make delta N-designs of other CH505 envelopes. In certain embodiments, the invention relates generally to an immunogen, gp160, gp120 or gp140, without an N-terminal Herpes Simplex gD tag substituted for amino acids of the N-terminus of gp120, with an HIV leader sequence (or other leader sequence), and without the original about 4 to about 25, for example 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 amino acids of the N-terminus of the envelope (e.g. gp120). See WO2013/006688, e.g. at pages 10-12, the contents of which publication is hereby incorporated by reference in its entirety.

The general strategy of deletion of N-terminal amino acids of envelopes results in proteins, for example gp120s, expressed in mammalian cells that are primarily monomeric, as opposed to dimeric, and, therefore, solves the production and scalability problem of commercial gp120 Env vaccine production. In other embodiments, the amino acid deletions at the N-terminus result in increased immunogenicity of the envelopes.

In certain embodiments, the invention provides envelope sequences, amino acid sequences and the corresponding nucleic acids, and in which the V3 loop is substituted with the following V3 loop sequence TRPNNNTRKSIRIGPGQTFY ATGDIIGNIRQAH (SEQ ID NO: 6). This substitution of the V3 loop reduced product cleavage and improves protein yield during recombinant protein production in CHO cells.

In certain embodiments, the CH505 envelopes will have added certain amino acids to enhance binding of various broad neutralizing antibodies. Such modifications could include but not limited to, mutations at W680G or modification of glycan sites for enhanced neutralization.

In certain aspects, the invention provides composition and methods which use a selection of sequential CH505 Envs, as gp120s, gp 140s cleaved and uncleaved, gp145s, gp150s and gp160s, stabilized and/or multimerized trimers, as proteins, DNAs, RNAs, or any combination thereof, administered as primes and boosts to elicit immune response. Sequential CH505 Envs as proteins would be co-administered with nucleic acid vectors containing Envs to amplify antibody induction. In certain embodiments, the compositions and methods include any immunogenic HIV-1 sequences to give the best coverage for T cell help and cytotoxic T cell induction. In certain embodiments, the compositions and methods include mosaic and/or consensus HIV-1 genes to give the best coverage for T cell help and cytotoxic T cell induction. In certain embodiments, the compositions and methods include mosaic group M and/or consensus genes to give the best coverage for T cell help and cytotoxic T cell induction. In some embodiments, the mosaic genes are any suitable gene from the HIV-1 genome. In some embodiments, the mosaic genes are Env genes, Gag genes, Pol genes, Nef genes, or any combination thereof. See e.g. U.S. Pat. No. 7,951,377. In some embodiments the mosaic genes are bivalent mosaics. In some embodiments the mosaic genes are trivalent. In some embodiments, the mosaic genes are administered in a suitable vector with each immunization with Env gene inserts in a suitable vector and/or as a protein. In some embodiments, the mosaic genes, for example as bivalent mosaic Gag group M consensus genes, are administered in a suitable vector, for example but not limited to HSV2, would be administered with each immunization with Env gene inserts in a suitable vector, for example but not limited to HSV-2.

In certain aspects the invention provides compositions and methods of Env genetic immunization either alone or with Env proteins to recreate the swarms of evolved viruses that have led to bnAb induction. Nucleotide-based vaccines offer a flexible vector format to immunize against virtually any protein antigen. Currently, two types of genetic vaccination are available for testing-DNAs and mRNAs.

In certain aspects the invention contemplates using immunogenic compositions wherein immunogens are delivered as DNA. See Graham B S, Enama M E, Nason M C, Gordon I J, Peel S A, et al. (2013) DNA Vaccine Delivered by a Needle-Free Injection Device Improves Potency of Priming for Antibody and CD8+ T-Cell Responses after rAd5 Boost in a Randomized Clinical Trial. PLoS ONE 8(4): e59340, page 9. Various technologies for delivery of nucleic acids, as DNA and/or RNA, so as to elicit immune response, both T-cell and humoral responses, are known in the art and are under developments. In certain embodiments, DNA can be delivered as naked DNA. In certain embodiments, DNA is formulated for delivery by a gene gun. In certain embodiments, DNA is administered by electroporation, or by a needle-free injection technologies, for example but not limited to Biojector® device. In certain embodiments, the DNA is inserted in vectors. The DNA is delivered using a suitable vector for expression in mammalian cells. In certain embodiments the nucleic acids encoding the envelopes are optimized for expression. In certain embodiments DNA is optimized, e.g. codon optimized, for expression. In certain embodiments the nucleic acids are optimized for expression in vectors and/or in mammalian cells. In non-limiting embodiments these are bacterially derived vectors, adenovirus based vectors, rAdenovirus (e.g. Barouch D H, et al. Nature Med. 16: 319-23, 2010), recombinant mycobacteria (e.g. rBCG or M smegmatis) (Yu, J S et al. Clinical Vaccine Immunol. 14: 886-093, 2007; ibid 13: 1204-11, 2006), and recombinant vaccinia type of vectors (Santra S. Nature Med. 16: 324-8, 2010), for example but not limited to ALVAC, replicating (Kibler K V et al., PLoS One 6: e25674, 2011 Nov. 9.) and non-replicating (Perreau M et al. J. virology 85: 9854-62, 2011) NYVAC, modified vaccinia Ankara (MVA)), adeno-associated virus, Venezuelan equine encephalitis (VEE) replicons, Herpes Simplex Virus vectors, and other suitable vectors.

In certain aspects the invention contemplates using immunogenic compositions wherein immunogens are delivered as DNA or RNA in suitable formulations. Various technologies which contemplate using DNA or RNA, or may use complexes of nucleic acid molecules and other entities to be used in immunization. In certain embodiments, DNA or RNA is administered as nanoparticles consisting of low dose antigen-encoding DNA formulated with a block copolymer (amphiphilic block copolymer 704). See Cany et al., Journal of Hepatology 2011 vol. 54 j 115-121; Arnaoty et al., Chapter 17 in Yves Bigot (ed.), Mobile Genetic Elements: Protocols and Genomic Applications, Methods in Molecular Biology, vol. 859, pp 293-305 (2012); Arnaoty et al. (2013) Mol Genet Genomics. 2013 August; 288(7-8):347-63. Nanocarrier technologies called Nanotaxi® for immunogenic macromolecules (DNA, RNA, Protein) delivery are under development. See for example technologies developed by incellart.

In certain aspects the invention contemplates using immunogenic compositions wherein immunogens are delivered as recombinant proteins. Various methods for production and purification of recombinant proteins, including trimers such as but not limited to SOSIP based trimers, suitable for use in immunization are known in the art. In certain embodiments recombinant proteins are produced in CHO cells.

The immunogenic envelopes can also be administered as a protein boost in combination with a variety of nucleic acid envelope primes (e.g., HIV-1 Envs delivered as DNA expressed in viral or bacterial vectors).

Dosing of proteins and nucleic acids can be readily determined by a skilled artisan. A single dose of nucleic acid can range from a few nanograms (ng) to a few micrograms (g) or milligram of a single immunogenic nucleic acid. Recombinant protein dose can range from a few g micrograms to a few hundred micrograms, or milligrams of a single immunogenic polypeptide.

Administration: The compositions can be formulated with appropriate carriers using known techniques to yield compositions suitable for various routes of administration. In certain embodiments the compositions are delivered via intramascular (IM), via subcutaneous, via intravenous, via nasal, via mucosal routes, or any other suitable route of immunization.

The compositions can be formulated with appropriate carriers and adjuvants using techniques to yield compositions suitable for immunization. The compositions can include an adjuvant, such as, for example but not limited to, alum, poly IC, MF-59 or other squalene-based adjuvant, ASOIB, or other liposomal based adjuvant suitable for protein or nucleic acid immunization. In certain embodiments, the adjuvant is GSK AS01E adjuvant containing MPL and QS21. This adjuvant has been shown by GSK to be as potent as the similar adjuvant AS01B but to be less reactogenic using HBsAg as vaccine antigen [Leroux-Roels et al., JABS Conference, April 2013]. In certain embodiments, TLR agonists are used as adjuvants. In other embodiment, adjuvants which break immune tolerance are included in the immunogenic compositions.

In certain embodiments, the compositions and methods comprise any suitable agent or immune modulation which could modulate mechanisms of host immune tolerance and release of the induced antibodies. In non-limiting embodiments modulation includes PD-1 blockade; T regulatory cell depletion; CD40L hyperstimulation; soluble antigen administration, wherein the soluble antigen is designed such that the soluble agent eliminates B cells targeting dominant epitopes, or a combination thereof. In certain embodiments, an immunomodulatory agent is administered in at time and in an amount sufficient for transient modulation of the subject's immune response so as to induce an immune response which comprises broad neutralizing antibodies against HIV-1 envelope. Non-limiting examples of such agents is any one of the agents described herein: e.g. chloroquine (CQ), PTP1B Inhibitor—CAS 765317-72-4—Calbiochem or MSI 1436 clodronate or any other bisphosphonate; a Foxo1 inhibitor, e.g. 344355 Foxo1 Inhibitor, AS1842856—Calbiochem; Gleevac, anti-CD25 antibody, anti-CCR4 Ab, an agent which binds to a B cell receptor for a dominant HIV-1 envelope epitope, or any combination thereof. In non-limiting embodiments, the modulation includes administering an anti-CTLA4 antibody. Non-limiting examples are ipilimumab and tremelimumab. In certain embodiments, the methods comprise administering a second immunomodulatory agent, wherein the second and first immunomodulatory agents are different.

There are various host mechanisms that control bNAbs. For example highly somatically mutated antibodies become autoreactive and/or less fit (Immunity 8: 751, 1998; PloS Comp. Biol. 6 e1000800, 2010; J. Thoret. Biol. 164:37, 1993); Polyreactive/autoreactive naïve B cell receptors (unmutated common ancestors of clonal lineages) can lead to deletion of Ab precursors (Nature 373: 252, 1995; PNAS 107: 181, 2010; J. Immunol. 187: 3785, 2011); Abs with long HCDR3 can be limited by tolerance deletion (JI 162: 6060, 1999; JCI 108: 879, 2001). BnAb knock-in mouse models are providing insights into the various mechanisms of tolerance control of MPER BnAb induction (deletion, anergy, receptor editing). Other variations of tolerance control likely will be operative in limiting BnAbs with long HCDR3s, high levels of somatic hypermutations.

Various antibodies names are used throughout the application. Below is listing of antibodies names correlation: CH490=CH235.6; CH491=CH235.7; CH492=CH235.8; CH493=CH235.9; CH555=CH235.10; CH556=CH235.11; CH557=CH235.12

TABLE 1 Summary of CH505 proteins and sequences. (1) See WO2014042669 (FIG. 17). gp120 chim.6R.SOSIP.664 chim.6R.DS.SOSIP.664 CHIM.6R.SOSIP.664V4.1 CHIM.- gp160 delta8 gp145 (SOSIP.I) (SIOSIP.I) (SOSIP.III) 6R.SOSIP.664V4.2 CH505 TF aa (1) (1) FIG. 23A FIG. 23A FIG. 23A FIG. 23A One (1) (1) embodiment of a nucleic acid W53.16 (1) (1) FIG. 23A FIG. 23A FIG. 23A FIG. 23A One (1) (1) embodiment of a nucleic acid W78.33 (1) (1) FIG. 23A FIG. 23A One (1) (1) embodiment of a nucleic acid W100.B6 (1) (1) FIG. 23A FIG. 23A One (1) (1) embodiment of a nucleic acid M5 aa FIG. 17B FIG. FIG. 19A FIG. 23A FIG. 23A 17A One embodiment of a nucleic acid M11 aa FIG. 17B FIG. FIG. 19A FIG. 23A FIG. 23A 19A One embodiment of a nucleic acid W20.14 aa FIG. 17B FIG. FIG. 19A FIG. 23A FIG. 23A 19A One embodiment of a nucleic acid W30.20 aa FIG. 17B FIG. FIG. 19A FIG. 23A FIG. 23A 19A One embodiment of a nucleic acid W30.12 aa FIG. 17B FIG. FIG. 19A FIG. 23A FIG. 23A 19A One embodiment of a nucleic acid W136.B18 aa FIG. 19B FIG. FIG. 19A FIG. 23A FIG. 23A 19A One embodiment of a nucleic acid W30.25 aa FIG. 17A FIG. 23A FIG. 23A One FIG. 17B embodiment of a nucleic acid W053.25 aa FIG. 17A FIG. 23A FIG. 23A One FIG. 17B embodiment of a nucleic acid W053.29 aa FIG. 17A FIG. 23A FIG. 23A One FIG. 17B embodiment of a nucleic acid

It is readily understood that the envelope glycoproteins referenced in various examples and figures comprise a signal/leader sequence. It is well known in the art that HIV-1 envelope glycoprotein is a secretory protein with a signal or leader peptide sequence that is removed during processing and recombinant expression (without removal of the signal peptide, the protein is not secreted). See for example Li et al. Control of expression, glycosylation, and secretion of HIV-1 gp120 by homologous and heterologous signal sequences. Virology 204(1):266-78 (1994) (“Li et al. 1994”), at first paragraph, and Li et al. Effects of inefficient cleavage of the signal sequence of HIV-1 gp120 on its association with calnexin, folding, and intracellular transport. PNAS 93:9606-9611 (1996) (“Li et al. 1996”), at 9609. Any suitable signal sequence could be used. In some embodiments the leader sequence is the endogenous leader sequence. Most of the gp120 and gp160 amino acid sequences include the endogenous leader sequence. In other non-limiting examples the leaders sequence is human Tissue Plasminogen Activator (TPA) sequence, human CD5 leader sequence (e.g. MPMGSLQPLATLYLLGMLVASVLA (SEQ ID NO: 7)). Most of the chimeric designs include CD5 leader sequence. A skilled artisan appreciates that when used as immunogens, and for example when recombinantly produced, the amino acid sequences of these proteins do not comprise the leader peptide sequences.

Nomenclature for trimers: chim.6R.DS.SOSIP.664 is SOSIP.I CHIM.6R.SOSIP.664 is SOSIP.II; CHIM.6R.SOSIP.664V4.1 is SOSIP.III.

The invention is described in the following non-limiting examples.

EXAMPLES Example 1

HIV-1 sequences, including envelopes, and antibodies from HIV-1 infected individual CH505 were isolated as described in Liao et al. (2013) Nature 496, 469-476 including supplementary materials; See also Gao et al. (2014) Cell 158:481-491.

Recombinant HIV-1 Proteins

HIV-1 Env genes for subtype B, 63521, subtype C, 1086, and subtype CRF_01, 427299, as well as subtype C, CH505 autologous transmitted/founder Env were obtained from acutely infected HIV-1 subjects by single genome amplification, codon-optimized by using the codon usage of highly expressed human housekeeping genes, de novo synthesized (GeneScript) as gp140 or gp120 (AE.427299) and cloned into a mammalian expression plasmid pcDNA3.1/hygromycin (Invitrogen). Recombinant Env glycoproteins were produced in 293F cells cultured in serum-free medium and transfected with the HIV-1 gp140- or gp120-expressing pcDNA3.1 plasmids, purified from the supernatants of transfected 293F cells by using Galanthus nivalis lectin-agarose (Vector Labs) column chromatography, and stored at −80° C. Select Env proteins made as CH505 transmitted/founder Env were further purified by superose 6 column chromatography to trimeric forms, and used in binding assays that showed similar results as with the lectin-purified oligomers.

ELISA

Binding of patient plasma antibodies and CH103, and DH235(CH235), See Gao et al. (2014) Cell 158:481-491, clonal lineage antibodies to autologous and heterologous HIV-1 Env proteins was measured by ELISA as described previously. Plasma samples in serial threefold dilutions starting at 1:30 to 1:521,4470 or purified monoclonal antibodies in serial threefold dilutions starting at 100 μg ml−1 to 0.000 μg ml−1 diluted in PBS were assayed for binding to autologous and heterologous HIV-1 Env proteins. Binding of biotin-labelled CH103 at the subsaturating concentration was assayed for cross-competition by unlabeled HIV-1 antibodies and soluble CD4-Ig in serial fourfold dilutions starting at 10 μg ml−1. The half-maximal effective concentration (EC50) of plasma samples and monoclonal antibodies to HIV-1 Env proteins were determined and expressed as either the reciprocal dilution of the plasma samples or concentration of monoclonal antibodies.

Surface Plasmon Resonance Affinity and Kinetics Measurements

Binding Kd and rate constant (association rate (Ka)) measurements of monoclonal antibodies and all candidate UCAs to the autologous Env C. CH05 gp140 and/or the heterologous Env B.63521 gp120 are carried out on BIAcore 3000 instruments as described previously. Anti-human IgG Fc antibody (Sigma Chemicals) is immobilized on a CM5 sensor chip to about 15,000 response units and each antibody is captured to about 50-200 response units on three individual flow cells for replicate analysis, in addition to having one flow cell captured with the control Synagis (anti-RSV) monoclonal antibody on the same sensor chip. Double referencing for each monoclonal antibody-HIV-1 Env binding interactions is used to subtract nonspecific binding and signal drift of the Env proteins to the control surface and blank buffer flow, respectively. Antibody capture level on the sensor surface is optimized for each monoclonal antibody to minimize rebinding and any associated avidity effects. C.CH505 Env gp140 protein is injected at concentrations ranging from 2 to 25 μg ml−1, and B.63521 gp120 was injected at 50-400 μg ml−1 for UCAs and early intermediates IA8 and IA4, 10-100 μg ml−1 for intermediate IA3, and 1-25 μg ml−1 for the distal and mature monoclonal antibodies. All curve-fitting analyses are performed using global fit of to the 1:1 Langmuir model and are representative of at least three measurements. All data analysis was performed using the BIAevaluation 4.1 analysis software (GE Healthcare).

Neutralization Assays

Neutralizing antibody assays in TZM-bl cells are performed as described previously. Neutralizing activity of plasma samples in eight serial threefold dilutions starting at 1:20 dilution and for recombinant monoclonal antibodies in eight serial threefold dilutions starting at 50 μg ml−1 are tested against autologous and herologous HIV-1 Env-pseudotyped viruses in TZM-bl-based neutralization assays using the methods known in the art. Neutralization breadth of CH103 is determined using a panel of 196 of geographically and genetically diverse Env-pseudoviruses representing the major circulated genetic subtypes and circulating recombinant forms. HIV-1 subtype robustness is derived from the analysis of HIV-1 clades over time. The data are calculated as a reduction in luminescence units compared with control wells, and reported as IC50 in either reciprocal dilution for plasma samples or in micrograms per microlitre for monoclonal antibodies.

The GenBank accession numbers for 292 CH505 Env proteins are KC247375-KC247667, and accessions for 459 V_(H)DJ_(H) and 174 V_(L)J_(L) sequences of antibody members in the CH103 clonal lineage are KC575845-KC576303 and KC576304-KC576477, respectively.

Example 2

Binding of sequential envelopes to CH103 and CH235 CD4 binding site bnAb lineages members.

The binding assay was an ELISA with the envelope protein bound to the well surface of a 96 well plate, and the antibody in questions incubated with the envelope bound to the plate. After washing, an enzyme-labeled anti-human IgG antibody was added and after incubation, washed away. The intensity of binding was determined by the intensity of enzyme-activated color in the well.

TABLE 2 ELISA binding, log-transformed area under the curve (AUC) values for a realization with four Env-derived gp120 antigens, assayed against members of the CH103 bnAb lineage from universal ancestor (UCA), through intermediate ancestors (IA8-IA1) to the mature bnAb. Values of 0 indicate no binding. The transmitted-founder (TF) antigen was derived from Env w004.3. Antigen UCA IA8 IA7 IA6 IA4 IA3 CH105 IA2 CH104 IA1 CH106 CH103 TF 3.5 5.5 9.2 9.1 10.1 11 11.2 10.8 10.4 10.4 11.3 12.6 w053.16 0 0 0 0 0.2 1.1 9 9.3 9.9 8.8 9.8 11.6 w078.33 0 0 0 0 0 0 8.9 9 9 8.2 9.5 11.1 w100.B6 0 0 0 0 0 0 11 12.1 11 12.2 11.8 7.1

TABLE 3 ELISA binding, log-transformed area under the curve (AUC) values for a realization with five Env-derived gp120 antigens, assayed against members of the CH103 bnAb lineage from universal ancestor (UCA), through intermediate ancestors (IA8-IA1) to the mature bnAb. Values of 0 indicate no binding. Antigen names beginning with M were synthesized by site-directed mutagenesis. Antigen UCA IA8 IA7 IA6 IA4 IA3 CH105 IA2 CH104 IA1 CH106 CH103 M11 2.6 6.2 10.1 10 10.5 11.8 11.7 12.7 12 12.2 12.8 13.4 M5 0 0.6 2.3 3.3 3.8 6.8 8.6 7.8 9 7 8.4 9.8 w020.14 0.3 3.4 7.2 7.9 8.6 9.5 10.4 11 10.4 10.3 11.2 12.6 w030.28 0 1.6 3.5 6.3 6.5 7.7 9.1 11.1 10.7 10.1 11.7 12.8 w078.15 0 0 0.7 1 1.3 3 10.1 11.5 10.8 10.9 11 10.7 w053.31 0 0 0 0 0 0 13.5 13.3 13.7 13.4 13.4 13.6

TABLE 4 ELISA binding, log-transformed area under the curve (AUC) values for a realization with five Env-derived gp120 antigens, assayed against members of the DH235 (CH235) bnAb helper lineage from universal ancestor (UCA), through intermediate ancestors (I4-I1) to mature bnAbs. Values of 0 indicate no binding. Antigen names beginning with M were synthesized by site-directed mutagenesis. Antigen UCA I4 I3 I2 I1 DH235 CH236 CH239 CH240 CH241 M11 0 0 0 0 2.8 7.6 1.4 1.4 0.5 9.7 M5 0.2 1.4 7 6.9 9.2 11.4 7.3 12.9 7.4 14.5 w020.14 0 0 2.7 1.2 6.5 9.9 6.7 9 3.8 13.1 w030.28 0 0 0 0 2.4 6.7 1.5 3.6 0.3 9.6 w078.15 0 0 0 0 0 0 0 0 0 0 w053.31 0 0 0 0 0 1.1 0 0 0 1.4

TABLE 5 ELISA binding, log-transformed area under the curve (AUC) values for a realization that embodies ten Env-derived gp120 antigens, assayed against members of the CH103 bnAb lineage from universal ancestor (UCA), through intermediate ancestors (IA8- IA1) to the mature bnAb. Values of 0 indicate no binding. Antigen names beginning with M were synthesized by site-directed mutagenesis. Antigen UCA IA8 IA7 IA6 IA4 IA3 CH105 IA2 CH104 IA1 CH106 CH103 M11 2.6 6.2 10.1 10 10.5 11.8 11.7 12.7 12 12.2 12.8 13.4 M5 0 0.6 2.3 3.3 3.8 6.8 8.6 7.8 9 7 8.4 9.8 w020.14 0.3 3.4 7.2 7.9 8.6 9.5 10.4 11 10.4 10.3 11.2 12.6 w030.28 0 1.6 3.5 6.3 6.5 7.7 9.1 11.1 10.7 10.1 11.7 12.8 w078.15 0 0 0.7 1 1.3 3 10.1 11.5 10.8 10.9 11 10.7 w053.16 0 0 0 0 0.2 1.1 9 9.3 9.9 8.8 9.8 11.6 w030.21 0 0 0 0 0 0 10.6 11.5 11.3 11.8 10.9 12.2 w078.33 0 0 0 0 0 0 8.9 9 9 8.2 9.5 11.1 w100.B6 0 0 0 0 0 0 11 12.1 11 12.2 11.8 7.1 w053.31 0 0 0 0 0 0 13.5 13.3 13.7 13.4 13.4 13.6

Example 3

Combinations of antigens derived from CH505 envelope sequences for swarm immunizations

Provided herein are non-limiting examples of combinations of antigens derived from CH505 envelope sequences for a swarm immunization. Without limitations, these selected combinations comprise envelopes which provide representation of the sequence and antigenic diversity of the HIV-1 envelope variants which lead to the induction and maturation of the CH103 and CH235 antibody lineages. The identification of bnAb lineage (CH103) and envelopes which bind preferentially to various members of this lineage provides a direct strategy for the selection of Envs (out of millions possible envelopes naturally occurring in an HIV-1 infected individual) that might have engaged UCA and participated in bnAb development, and thus could serve as immunogens in a vaccine formulation. The identification of helper lineage (CH235) and envelopes which bind preferentially to various members this lineage provides a direct strategy for the selection of Envs (out of millions possible envelopes naturally occurring in an HIV-1 infected individual) that might have engaged UCA and participated in bnAb development, and thus could serve as immunogens in a vaccine formulation.

The selection includes priming with a virus which binds to the UCA, for example a T/F virus or another early (e.g. but not limited to week 004.3, or 004.26) virus envelope. In certain embodiments the prime could include D-loop variants. In certain embodiments the boost could include D-loop variants. In certain embodiments, these D-loop variants are envelope escape mutants not recognized by the UCA. Non-limiting examples of such D-loop variants are envelopes designated as M10, M11, M19, M20, M21, M5, M6, M7, M8, M9, M14 (TF_M14), M24 (TF_24), M15, M16, M17, M18, M22, M23, M24, M25, M26. See Gao et al. (2014) Cell 158:481-491.

Non-limiting embodiments of envelopes selected for swarm vaccination are shown as the selections described below. A skilled artisan would appreciate that a vaccination protocol can include a sequential immunization starting with the “prime” envelope(s) and followed by sequential boosts, which include individual envelopes or combination of envelopes. In another vaccination protocol, the sequential immunization starts with the “prime” envelope(s) and is followed with boosts of cumulative prime and/or boost envelopes. In certain embodiments, the sequential immunization starts with the “prime” envelope(s) and is followed by boost(s) with all or various combinations of the envelopes in the selection. In certain embodiments, the prime does not include T/F sequence (W000.TF). In certain embodiments, the prime includes w004.03 envelope. In certain embodiments, the prime includes w004.26 envelope. In certain embodiment the prime includes M11. In certain embodiments the prime includes M5. In certain embodiments, the immunization methods do not include immunization with HIV-1 envelope T/F. In certain embodiments, the immunization methods do not include a schedule of four valent immunization with HIV-1 envelopes T/F, w053.16, w078.33, and w100.B6.

In certain embodiments, there is some variance in the immunization regimen; in some embodiments, the selection of HIV-1 envelopes may be grouped in various combinations of primes and boosts, either as nucleic acids, proteins, or combinations thereof.

In certain embodiments the immunization includes a prime administered as DNA, and MVA boosts. See Goepfert, et al. 2014; “Specificity and 6-Month Durability of Immune Responses Induced by DNA and Recombinant Modified Vaccinia Ankara Vaccines Expressing HIV-1 Virus-Like Particles” J Infect Dis. 2014 Feb. 9. [Epub ahead of print].

HIV-1 Envelope selection A (five envelopes): M11; w020.14; w030.28; w078.15; w053.31

HIV-1 Envelope selection B (six envelopes): M11; M5; w020.14; w030.28; w078.15; w053.31

HIV-1 Envelope selection C (ten envelopes): M11; M5; w020.14; w030.28; w078.15; w053.16; w030.21; w078.33; w100.B6; w053.31.

HIV-1 Envelopes selection D (six envelopes): M5, M11, 20.14, 30.28, 30.23, 136.B18.

HIV-1 Envelopes selection E (six envelopes): M5, M11, 20.14, 30.20, 30.23, 136.B18.

HIV-1 Envelopes selection F (six envelopes—P186 study): M5, M11, 20.14, 30.20, 30.12, 136.B18.

HIV-1 envelope selection G (EnvSeq-2): M5, 30.25; 53.25; 53.29.

HIV-1 envelope selection H (EnvSeq-3): M5, 30.20; 20.14, 30.12.

Selections using M5 as a prime, e.g. but not limited to D, E, F, G or H are expected to engage receptors and drive progression of CH235 lineage of antibodies.

The selections of CH505-Envs were down-selected from a series of 400 CH505 Envs isolated by single-genome amplification followed for 3 years after acute infection, based on experimental data. The enhanced neutralization breadth that developed in the CD4-binding site (bs) CH103 antibody lineage that arose in subject CH505 developed in conjunction with epitope diversification in the CH505's viral quasispecies. It was observed that at 6 months post-infection there was more diversification in the CD4bs epitope region in this donor than sixteen other acutely infected donors. Population breadth did not arise in the CH103 antibody lineage until the epitope began to diversify. A hypothesis is that the CH103 linage drove viral escape, but then the antibody adapted to the relatively resistant viral variants. As this series of events was repeated, the emerging antibodies evolved to tolerate greater levels of diversity in relevant sites, and began to be able to recognize and neutralize diverse heterologous forms for the virus and manifest population breadth. In certain embodiments, six envs are selected from CH505 sequences to reflect diverse variants for making Env pseudoviruses, with the goal of recapitulating CH505 HIV-1 antigenic diversity over time, making sure selected site (i.e. those sites reflecting major antigenic shifts) diversity was represented.

Specifically, for CH505 the virus and envelope evolution were mapped, and the CH103 CD4 binding-site bnAb evolution. In addition, 135 CH505 varied envelope pseudotyped viruses were made and tested them for neutralization sensitivity by members of the CH103 bnAb lineage (e.g, FIG. 3). From this large dataset, in one embodiment, six Env variants were chosen for immunization based on sequence diversity, and antigenic diversity, for example binding to antibodies in the CH103 and/or CH235 lineage (Tables 3-5).

In certain embodiments, the envelopes are selected based on Env mutants with sites under diversifying selection, in which the transmitted/founder (T/F) Env form vanished below 20% in any sample, i.e. escape variants; signature sites based on autologous neutralization data, i.e. Envs with statistically supported signatures for escape from members of the CH103 bnAb lineage; and sites with mutations at the contact sites of the CH103 antibody and HIV Env. In this manner, a sequential swarm of Envs was selected for immunization to represent the progression of virus escape mutants that evolved during bnAb induction and increasing neutralization breadth in the CH505 donor.

In certain embodiments, additional sequences are selected to contain five additional specific amino acid signatures of resistance that were identified at the global population level. These sequences contain statistically defined resistance signatures, which are common at the population level and enriched among heterologous viruses that CH103 fails to neutralize. When they were introduced into the TF sequence, they were experimentally shown to confer partial resistance to antibodies in the CH103 lineage. Following the reasoning that serial viral escape and antibody adaptation to escape is what ultimate selects for neutralizing antibodies that exhibit breadth and potency against diverse variants, in certain embodiments, inclusion of these variants in a vaccine may extend the breadth of vaccine-elicited antibodies even beyond that of the CH103 lineage. Thus the overarching goal will be to trigger a CH103-like lineage first using the CH505TF modified M11, that is well recognized by early CH103 ancestral states, then vaccinating with antigenic variants, to allow the antibody lineage to adapt through somatic mutation to accommodate the natural variants that arose in CH505. In certain embodiments, vaccination regimens include a total of five sequences (Selection A) that capture the antigenic diversity of CH505. In another embodiment, additional antigenic diversity is added (Selection B and C), to enable the induction of antibodies by vaccination that may have even greater breadth than those antibodies isolated from CH505.

In some embodiments, the CH505 sequences that represent the accumulation of viral sequence and antigenic diversity in the CD4bs epitope of CH103 in subject CH505 are represented by selection A, selection B, or selection C.

M11 is a mutant generated to include two mutations in the loop D (N279D+V281G relative to the TF sequence) that enhanced binding to the CH103 lineage. These were early escape mutations for another CD4bs autologous neutralizing antibody lineage, but might have served to promote early expansion of the CH103 lineage.

In certain embodiments, the two CH103 resistance signature-mutation sequences added to the antigenic swarm are: M14 (TF with S364P), and M24 (TF with S375H+T202K+L520F+G459E). They confer partial resistance to the TF with respect to the CH103 lineage. In certain embodiments, these D-loop mutants are administered in the boost.

Example 4

Immunization protocols in subjects with swarms of HIV-1 envelopes.

Immunization protocols contemplated by the invention include envelopes sequences as described herein including but not limited to nucleic acids and/or amino acid sequences of gp160s, gp150s, gp145, cleaved and uncleaved gp140s, stabilized trimers, e.g. but not limited to SOSIP trimers, gp120s, gp41s, N-terminal deletion variants as described herein, cleavage resistant variants as described herein, or codon optimized sequences thereof. A skilled artisan can readily modify the gp160 and gp120 sequences described herein to obtain these envelope variants. The swarm immunization selections can be administered in any subject, for example monkeys, mice, guinea pigs, or human subjects.

In non-limiting embodiments, the immunization includes a nucleic acid which is administered as DNA, for example in a modified vaccinia vector (MVA). In non-limiting embodiments, the nucleic acids encode gp160 envelopes. In other embodiments, the nucleic acids encode gp120 envelopes. In other embodiments, the boost comprises a recombinant gp120 envelope. The vaccination protocols include envelopes formulated in a suitable carrier and/or adjuvant, for example but not limited to alum. In certain embodiments the immunizations include a prime, as a nucleic acid or a recombinant protein, followed by a boost, as a nucleic acid or a recombinant protein. A skilled artisan can readily determine the number of boosts and intervals between boosts.

In some embodiments, the immunization methods comprise immunization prime with a nucleic acid, for example but not limited to priming two times with DNA. In some embodiments the nucleic acid prime is administered one, two, three or four times. In some embodiments the two DNA prime is administered via electroporation (DNA-EP). In some embodiments, the primer and boost is administered as RNA. The primes are followed by boost with sequential envelopes. The boosting envelopes could be in any suitable form, e.g. but not limited to gp140s, as soluble or stabilized SOSIP trimers.

Table 6 shows a non-limiting example of an immunization protocol using a selection of HIV-1 envelopes

Envelope Prime Boost(s) Boost(s) Boost(s) M11 M11 as a nucleic acid e.g. DNA/MVA vector and/or protein W020.14 W020.14 as a nucleic acid e.g. DNA/MVA and/or protein W030.28 W030.28 as nucleic acid e.g. DNA/MVA and/or protein W078.15 w078.15 as nucleic acid e.g. DNA/MVA and/or protein W100.B6 W100.B6 as nucleic acid e.g. DNA/MVA and/or protein

Table 7 shows a non-limiting example of an immunization protocol using a selection of HIV-1 envelopes

Envelope Prime Boost(s) Boost(s) Boost(s) M11 M11 as a M11 as a M11 as a M11 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA vector DNA/MVA vector DNA/MVA vector DNA/MVA vector and/or protein and/or protein and/or protein and/or protein W020.14 W020.14 as a W020.14 as a W020.14 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA DNA/MVA and/or protein and/or protein and/or protein W030.28 W030.28 as W030.28 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W078.15 w078.15 as w078.15 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W100.B6 W100.B6 as nucleic acid e.g. DNA/MVA and/or protein

In certain embodiments, after administering a prime with M11, subsequent immunizations include all other envelopes as nucleic acids and/or proteins.

Table 8 shows a non-limiting example of an immunization protocol using a swarm of HIV-1 envelopes

Envelope Prime Prime/Boost Boost(s) Boost(s) Boost(s) M11 M11 as a nucleic acid e.g. DNA/MVA vector and/or protein M5 M5 as a nucleic acid e.g. DNA/MVA and/or protein W020.14 W020.14 as a nucleic acid e.g. DNA/MVA and/or protein W030.28 W030.28 as nucleic acid e.g. DNA/MVA and/or protein W078.15 w078.15 as nucleic acid e.g. DNA/MVA and/or protein W100.B6 W100.B6 as nucleic acid e.g. DNA/MVA and/or protein

Table 9 shows anon-limiting example of an immunization protocol using a swarm of HIV-1 envelopes

Envelope Prime Prime/Boost Boost(s) Boost(s) Boost(s) M11 M11 as a M11 as a M11 as a M11 as a M11 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA vector DNA/MVA vector DNA/MVA vector DNA/MVA vector DNA/MVA vector and/or protein and/or protein and/or protein and/or protein and/or protein M5 Optionally M5 as a M5 as a M5 as a M5 as a M5 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA DNA/MVA DNA/MVA DNA/MVA and/or protein and/or protein and/or protein and/or protein and/or protein W020.14 W020.14 as a W020.14 as a W020.14 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA DNA/MVA and/or protein and/or protein and/or protein W030.28 W030.28 as W030.28 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W078.15 w078.15 as w078.15 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W100.B6 W100.B6 as nucleic acid e.g. DNA/MVA and/or protein

In certain embodiments, after administering a prime with M11 and optionally with M5, subsequent immunizations include all other envelopes as nucleic acids and/or proteins.

Table 10 shows a non-limiting example of immunization protocol using a selection of ten HIV-1 envelopes

Envelope Prime Prime/Boost Boost(s) Boost(s) Boost(s) Boost(s) Boost(s) Boost(s) Boost(s) M11 M11 as a nucleic acid e.g. DNA/MVA vector and/or protein M5 M5 as a nucleic acid e.g. DNA/MVA and/or protein W020.14 W020.14 as a nucleic acid e.g. DNA/MVA and/or protein W030.28 W030.28 as nucleic acid e.g. DNA/MVA and/or protein W078.15 w078.15 as nucleic acid e.g. DNA/MVA and/or protein W053.16 W053.16 as nucleic acid e.g. DNA/MVA and/or protein W030.21 W030.21 as nucleic acid e.g. DNA/MVA and/or protein W078.33 W078.33 as nucleic acid e.g. DNA/MVA and/or protein W100.B6 W100.B6 as nucleic acid e.g. DNA/MVA and/or protein W053.31 W053.31 as nucleic acid e.g. DNA/MVA and/or protein

Table 11 shows anon-limiting example of immunization protocol using a selection of six HIV-1 envelopes

Envelope Prime Prime/Boost Boost(s) Boost(s) Boost(s) M11 M11 as a M11 as a M11 as a M11 as a M11 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA vector DNA/MVA vector DNA/MVA vector DNA/MVA vector DNA/MVA vector and/or protein and/or protein and/or protein and/or protein and/or protein M5 Optionally M5 as a M5 as a M5 as a M5 as a M5 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA DNA/MVA DNA/MVA DNA/MVA and/or protein and/or protein and/or protein and/or protein and/or protein W020.14 W020.14 as a W020.14 as a W020.14 as a nucleic acid e.g. nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA DNA/MVA and/or protein and/or protein and/or protein W030.20 W030.20 as W030.20 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W030.12 w030.12 as w030.12 as nucleic acid e.g. nucleic acid e.g. DNA/MVA DNA/MVA and/or protein and/or protein W136.B18 W136.B18 as nucleic acid e.g. DNA/MVA and/or protein

Table 12 shows anon-limiting example of immunization protocol using a selection of six HIV-1 envelopes

Envelope Prime Boost(s) Boost(s) Boost(s) Boost(s) M11 M11 as a nucleic acid e.g. DNA/MVA vector and/or protein M5 Optionally M5 as a nucleic acid e.g. DNA/MVA and/or protein W020.14 W020.14 as a nucleic acid e.g. DNA/MVA and/or protein W030.20 W030.20 as nucleic acid e.g. DNA/MVA and/or protein W030.12 w030.12 as nucleic acid e.g. DNA/MVA and/or protein W136.B18 W136.B18 as nucleic acid e.g. DNA/MVA and/or protein

In certain embodiments, after administering a prime with M11 and optionally with M5, subsequent immunizations include sequential or cumulative addition of the other envelopes as nucleic acids and/or proteins.

Table 13 shows anon-limiting example of immunization protocol using a selection of four HIV-1 envelopes

Envelope Prime Boost(s) Boost(s) Boost(s) M5 M5as a nucleic acid e.g. DNA/MVA vector and/or protein W30.25 W30.25 as a nucleic acid e.g. DNA/MVA vector and/or protein W53.25 W53.25 as a nucleic acid e.g. DNA/MVA vector and/or protein W53.29 W53.29 as a nucleic acid e.g. DNA/MVA vector and/or protein

In certain embodiments an immunization protocol could prime with a bivalent or trivalent Gag mosaic (Gag1 and Gag 2, Gag 1, Gag 2 and Gag3) in a suitable vector.

Example 5

Env mixtures of the CH505 virus are expected to induce the beginning of CD4 binding site BnAb lineages CH103 and CH235

The combinations of envelopes described in Examples 2-4 will be tested in any suitable subject. Suitable animal models include without limitation mice, including humanized mice, guinea pigs, or non-human primates (NHPs). For example an animal is administered with the following antigens, as DNA and/or proteins, in any suitable for, in the following immunization schedule: Prime: loop D mutant M5 and M11. That will give the best CH103 UCA binder (M11) and the best CH235 UCA binder (M5). Immunization 2: week 020.14. Immunization 3: Week 030.28. Immunization 4: week 078.15. Immunization 5: week 100.B6. Immunization 5: swarm of all six envelopes. Adjuvant is a TLR-4 agonist (GLA-synthetic monophosphoryl lipid A) in stable emulsion from Infectious Disease Research Institute, Seattle Wash.

In another embodiment, the prime is M5 and M11. The boost includes 20.14, 30.20, 30.12, and 136.B18, sequentially or additively.

Example 5A

Immunization elicits heterologous and autologous Tier 2 neutralizing antibodies.

While improved breadth of vaccine-induced neutralizing antibody responses against tier 2 viruses are needed for a protective HIV-1 vaccine, elicitation of bnAbs by vaccination has proven challenging.

This example shows elicitation of heterologous and autologous tier 2 neutralizing antibodies with sequential Env vaccination in rhesus macaques. See also FIGS. 25-34. The method comprised administering T/F envelope as gp145 DNA via electroporation, followed by boosting with T/F, w053.16, w078.33 and w100.B6 envelopes administered as gp140C envelopes.

Co-evolution studies of the CH103 lineage of antibodies and viruses from the same infected person CH505 provides a roadmap for how bnAbs develop during natural infection (Liao et al. Nature 2014; Bonsignori et al. Cell 2016).

This animal study compared the immunogenicity of CH505 gp140C oligomers to CH505-CD40 conjugates. We hypothesize that a roadblock to bnAb induction by vaccination is the lack of B cell stimulation by antigen presenting cells (dendritic cells and monocytes), and that bNAbs, similar to those in the CH103 bnAb lineage, can be induced by vaccination with sequential Envs from CH505 (TF, w053.16, w078.33 and w100.B6). In this experiment the T/F envelope was administered as a DNA prime. In some animals the boosting envelopes (TF, w053.16, w078.33 and w100.B6) were administered as gp140C envelopes. In some animals these envelopes were targeted to antigen presenting cells by a CD40 antibody—human anti-CD40 IgG4 was linked to the CH505 gp140C.

It is possible that the reduced immunogenicity of the anti-CD40 IgG4-CH505 Env regimen is due to anti-drug antibodies in rhesus macaques.

This example shows that: DNA-EP prime and gp140C oligomer boosts induced autologous tier 2 neutralization in 1 of 4 macaques; heterologous tier 2 neutralization of 9/12 tier 2 isolates was also elicited in the same macaque; and that CD4 binding site directed plasma IgG was present in wildtype Env immunized macaques. RSC3-reactive B cells were sorted from macaques and the binding and neutralization screening is ongoing.

This example demonstrated that sequential Env immunogens, including the sequential immunogens used in this study could induce heterologous Tier 2 neutralizatoin. One alternative to increase the response rate of bnAb induction is the use of sequential near-native soluble CH505 trimers (e.g. but not limited to SOSIP based trimers as described herein). Immunization with CH505 stabilized trimers while modulating immune tolerance with immune checkpoint inhibitors is also underway.

In some embodiments, the immunization methods could comprise immunization prime with a nucleic acid, for example but not limited to priming two times with DNA, In some embodiments the nucleic acid prime is administered one, two, three or four times. In some embodiments the two DNA prime is administered via electroporation (DNA-EP). In some embodiments the nucleic acid encodes any suitable form of the envelope. In some embodiments, the primer and boost is administered as RNA. The primes are followed by boost with sequential envelopes. The boosting envelopes could be in any suitable form, e.g. but not limited to gp140s, as soluble or stabilized SOSIP trimers, e.g. but not limited to SOSIP.III.

Example 6

Over the past five years, the HIV vaccine development field has realized that immunization with a single HIV envelope protein will not be successful at inducing bnAbs^(1,2). Moreover, with evidence for a role of host immune tolerance control mechanisms in limiting the induction of bnAbs^(1,3), the biology of bnAbs has begun to be elucidated. The role of the structure of the Env immunogen is undoubtedly important, as the Env must contain sufficiently native bnAb epitopes to bind in optimal affinities to the unmutated common ancestor (UCA, naïve B cell receptors) of bnAb lineages^(2,4). Thus, the concept of B cell lineage immunogen design has arisen, whereby lineages of bnAbs are elucidated, and Envs chosen for sequential immunizations based on optimized affinity of Env immunogens for BCRs at sequential steps of the affinity maturation pathway of bnAb lineages²

While Envs have been designed for reacting with UCAs of heterologous bnAb lineages^(4,5), we have taken the approach of defining, in select HIV-infected individuals who make bnAbs, the natural sequence of Envs that induced the bnAb lineages in order to make immunogen down selection an evidence-based decision. While such immunogens are designed for the UCA and intermediate antibodies of one particular bnAb lineage, they hold promise for inducing bnAb lineages in multiple individuals because of the remarkable conserved usage of VH and VL genes of bnAbs and the restricted nature of antibody motifs for many bnAb types, particularly for the gp41 membrane proximal region⁶, the CD4 binding site⁷ and the V1V2-glycan site^(1,8-10).

Two Types of CD4 Binding Site Antibodies

There are several types of CD4 binding site (bs) bnAbs two of which are a) heavy chain complementarity determining region 3 (HCDR3) binders and b) CD4 mimicking bnAbs⁷. HCDR3 binding CD4 binding site bnAbs approach the CD4 binding site with the HCDR3 and other VH and VL loops with multiple loop-based interactions. Several different VHs and VLs are used by HCDR3 binding bnAbs with VH3 and VH4 the most common. In contrast, CD4 mimicking bnAbs have restricted VH usage and either use VH1-2*02 or VH1-46. When VH1-2*02 is used, the light chain LCDR3 must be five amino acids in length. However, when VH1-46 is used, the LCDR3 can be of normal (10-13 aa) in length. Both VH1-2*02 and VH1-46 CD4 mimicking antibodies approach the CD4 binding site in a highly homologous manner to the approach of CD4, and structural analysis of such bnAbs demonstrates both structural similarity to CD4, as well as near identical structures to each of these types of antibodies⁷. Finally, HCDR3 binders are less broad and potent than CD4 mimicking antibodies, with HCDR3 binders neutralizing ˜50% of isolates (e.g., CH103, CH98) while CD4 mimickers neutralizing 90-95% of isolates (e.g., CH235.12, VRC01)⁷. Thus, both types of antibodies are desirable to induce with vaccination as components of a polyclonal bnAb response.

The CH505 African HIV-infected individual that makes both types of CD4bs bnAbs over 6 years (See Liao et al. (2013) Nature 496, 469-476 including supplementary materials; See also Gao et al. (2014) Cell 158:481-491; Example 8)

Thus, from African individual CH505, we have isolated both sequential Envs and bnAbs over time, and mapped the co-evolution of two bnAb lineages, the CH103 CD4 binding site HCDR3 binder bnAb lineage¹¹ and the CH235 CD4 mimicking CD4bs VH1-46 bnAb lineage¹². The CH103 HCDR3 binder type of CD4 binding site antibody achieved 55% maximum breadth and 4.5 mcg inhibitory concentration 50 (IC50) neutralization of cross-clade HIVs¹¹. In contrast, the CH235 CD4 mimicking CD4 binding site antibody achieved 90% neutralization and neutralizing IC50 of 0.7 mcg/ml. Here, we will describe the work of development of sequential Env regimens to induce both of these types of bnAb lineages, and propose here the new sequential Envs to specifically initiate CH235-like CD4 mimicking bnAb lineages.

The EnvSeq-1 Sequential Vaccine from CH505 Designed to Induce HCDR3-Type of CD4 Binding Site bnAbs

We have developed a 4-valent immunogen comprised of CH505 envelopes that have been designed to trigger the CH103 lineage UCA to clonally expand and start off CH103-like CD4bs HCDR3-binder types of B cell lineages (TF; w053.16; w078.33; w100.B6 the EnvSeq-1 vaccine, see WO2014042669 incorporated by reference in its entirety). In SPR assays, the transmitted/founder (T/F) Env gp120 reacted with the UCA of the CH103 lineage with a K_(D) of ˜200 nM. Studies in CH103 VH+VL knock-in mice and Rhesus macaques using EnvSeq-1 have been completed and demonstrate proof of concept that sequential CH505 gp120s can initiate bnAb B cell clonal lineages in the setting of vaccination. The EnvSeq-1 vaccine binds to CH103 precursors in CH103 bnAb knock-in mice and can expand them with immunization in adjuvant. In Rhesus macaques, the gp120 EnvSeq-1 vaccine can induce antibodies with the characteristics of precursors of CD4 binding site bnAbs. These characteristics include antibodies that differentially bind CH505 Env but not Env with an isoleucine deletion at aa 371 that disrupts the CD4 binding site, antibodies that use similar VH4 and V13 genes to the human CH103 bnAb, and antibodies that neutralize the tier 1b T/F variant CH505 4.3 as well as some tier 2 viruses.

Utility of gp120s as Sequential Envs

Whether a native trimer is needed for this purpose or if a highly antigenic Env subunit will suffice is yet unknown, but studies in mice in basic B cell biology have demonstrated that what is important for B cell survival in the germinal center (GC) is the optimal affinity of the immunogen for the GC B cell receptor (BCR)^(13,14). A key question is whether gp120 or gp140 trimers are preferred immunogens in a sequential regimen. Emerging data have demonstrated that gp120s or their fragments can engage bnAb UCAs and expand CD4bs bnAb precursors^(5,15,16). In contrast, recent data with soluble individual trimers have demonstrated that they have only induced autologous tier 2 neutralizing antibodies against glycan-bare spots and not bnAb epitopes^(17,18). Thus, it is appropriate at this time to continue to study gp120 immunogens in man to test the hypothesis that sequential immunogens can initiate bnAb lineages. Whether boosting later in the immunization sequence with a trimeric Env will be needed will be tested in future studies.

The EnvSeq-2 Sequential Vaccine from CH505 is Designed to Induce CD4 Mimicking-Type of CD4 Binding Site bnAbs

In this application we propose to extend the test of sequential Env immunizations in man for initiation of broadly neutralizing antibodies to test in a human Phase I clinical trial of a new series of CH505 Envs (the EnvSeq-2 vaccine) specifically designed to induce a more broad and potent bnAb type, the CH235-like VH1-46 utilizing CD4 mimicking broad neutralizing antibody with 90% breadth and 0.6 mcg/ml inhibitory concentration 50 (IC50).

Design of a Sequential Immunogen (EnvSeq-2) to Initiate VH1-46 CD4 Mimicking CD4 Binding Site Antibody Lineages

Provided herein is a new set of immunogens based on the recent work describing the sequence of events that occurred with the development of CD4 mimicking CD4 binding site bnAb lineage, CH235¹².

From this work, a natural mutant of the CH505 T/F Env called CH505.M5 was found with one amino acid difference than the CH505 T/F strain, i.e., a single N279K change, that occurred very early on after infection; M5 binds to the CH235 UCA (˜0.5 micromolar)³. Thus, M5 is the initiating Env for CD4 mimicking CD4 binding site antibodies in the context of the EnvSeq-2 vaccine.

Next, a set of 6 mutations at amino acids 97, 275, 278, 279, 281, and 471 in the Env binding site to the CH235 lineage (FIG. 10), that were associated with escape from early CH235 antibody lineage members from autologous CH505 viruses were identified and three additional Envs chosen based on mutations at these sites.

TABLE 14 EnvSeq-2 vaccine and key amino acid mutations as well as V5 length in vaccine Env gp120 components. Vaccine Env aa97 aa275 aa279 aa281 aa471 Env V5 length CH505 M5 K E T V G 8 CH505 30.25 K E T A G 10 CHO505 53.35 E E T G G 11 CH505 53.29 K E T A E 11

Importantly, the later CH235 antibody lineage members acquired the ability to recognize viruses with these 6 Env mutations, presumably due to the selection imposed by exposure to the resistance mutations in vivo. These late Ch235 antibodies (such as the most potent CH235.12 antibody) had expanded breadth due to selection for recognition of these 6 mutations.

These chosen Envs in EnvSeq-2 vaccine are not associated with the best binding of the antibodies at intermediate steps as was done for design of the EnvSeq-1 vaccine above. Rather, as the increase in breadth at in the heterologous panel coincided with a gained capacity to recognize resistance mutations, Envs were selected based on their potential to expand CH235 antibody lineage recognition in order to tolerate these 6 key and common neutralization resistance-Env mutations. Nonetheless the selected Envs indeed had capacity to sequentially bind to lineage members (FIG. 20).

Finally, the fifth hypervariable loop (V5) region length was also a strong signature for recognition of CH505 viruses by CH235 antibodies, and early lineage members could only bind and neutralize short V5s. Longer V5s were selected by the early antibodies, and later antibodies could recognize viruses with longer V5s, which are more representative of the heterologous tier 2 HIV virus population. Thus, a final key criterion for selection of sequential Envs in the EnvSeq-2 vaccine was progressive lengthening of V5 (Table 14). Thus, the EnvSeq-2 Envs are associated with development of heterologous breadth from the CH235 UCA→CH235→CH235.9→CH235.12.

The EnvSeq-2 set of immunogens are currently begin produced in non-GMP in pre-production runs, and during year 1 of the Staged Vaccine Contract, will be tested in vitro in recombinant protein immunizations in both VH+VL humanized mice and rhesus macaques. In addition, a second set of CH505 immunogens chosen based on affinity of binding to members of the CH235 antibody lineage will be tested in similar immunization studies (a vaccine called EnvSeq-3, FIG. 21).

The optimal immunogen of the two sets of sequential Envs following comparison of EnvSeq-2 versus EnvSeq-3 will be chosen for GMP production in preclinical studies based on the following criteria:

-   -   a) highest level of induction of memory B cell antibodies that         bind to CH505 Env and do not bind to CH505 Env with an         isoleucine deletion at amino acid position 371 that disrupts the         CD4 binding site (called “differential binding” memory B cells),     -   b) no neutralization of the tier 2 CH505 T/F virus (the CH235         UCA does not neutralize the CH505 tier 2 TF virus. However, if         the induced antibodies do neutralize the tier 2 TF CH505 virus,         then it will be an indication of immunogen driving a CH235         lineage further into lineage maturation).     -   c) highest level of neutralization of the tier 1b CH505 T/F         variant 4.3,     -   d) highest level of heterologous primary HIV strain neutralizing         antibodies induced.

In summary, provided are two selections of CH505 envelopes—FIG. 20 (EnvSeq-2) or FIG. 21(EnvSeq-3)—for use in immunization regimens. In some embodiments these are used as recombinant CH505 Env gp120s (including gp120 delta N)), to be used in sequence following the administration of the CH505 M5 priming Env that binds to the CH235 UCA. In other embodiments these are used in any other suitable form, for example but not limited to stable SOSIP trimer designs, gp145s, gp140s, both cleaved and uncleaved, gp140 Envs with the deletion of the cleavage (C) site, fusion (F) and immunodominant (I) region in gp41—named as gp140ΔCFI (g140CFI), gp140 Envs with the deletion of only the cleavage (C) site and fusion (F) domain—named as gp140ΔCF (gp140CF), gp140 Envs with the deletion of only the cleavage (C)—named gp140AC (gp140C) (See e.g. Liao et al. Virology 2006, 353, 268-282), gp150s, gp41s, which are readily derived from the nucleic acid and amino acid gp160 sequences.

References for Example 6:

-   1 Mascola, J. R. & Haynes, B. F. HIV-1 neutralizing antibodies:     understanding nature's pathways. Immunological reviews 254, 225-244,     doi:10.1111/imr.12075 (2013). -   2 Haynes, B. F., Kelsoe, G., Harrison, S. C. & Kepler, T. B.     B-cell-lineage immunogen design in vaccine development with HIV-1 as     a case study. Nature biotechnology 30, 423-433, doi:10.1038/nbt.2197     (2012). -   3 Haynes, B. F. & Verkoczy, L. AIDS/HIV. Host controls of HIV     neutralizing antibodies. Science 344, 588-589,     doi:10.1126/science.1254990 (2014). -   4 Jardine, J. et al. Rational HIV immunogen design to target     specific germline B cell receptors. Science 340, 711-716,     doi:10.1126/science.1234150 (2013). -   McGuire, A. T. et al. Engineering HIV envelope protein to activate     germline B cell receptors of broadly neutralizing anti-CD4 binding     site antibodies. The Journal of experimental medicine 210, 655-663,     doi:10.1084/jem.20122824 (2013). -   6 Morris, L. et al. Isolation of a human anti-HIV gp41 membrane     proximal region neutralizing antibody by antigen-specific single B     cell sorting. PloS one 6, e23532, doi:10.1371/journal.pone.0023532     (2011). -   7 Zhou, T. et al. Structural Repertoire of HIV-1-Neutralizing     Antibodies Targeting the CD4 Supersite in 14 Donors. Cell 161,     1280-1292, doi:10.1016/j.cell.2015.05.007 (2015). -   8 Bonsignori, M. et al. Analysis of a clonal lineage of HIV-1     envelope V2/V3 conformational epitope-specific broadly neutralizing     antibodies and their inferred unmutated common ancestors. Journal of     virology 85, 9998-10009, doi:10.1128/JVI.05045-11(2011). -   9 Andrabi, R. et al. Identification of Common Features in Prototype     Broadly Neutralizing Antibodies to HIV Envelope V2 Apex to     Facilitate Vaccine Design. Immunity 43, 959-973,     doi:10.1016/j.immuni.2015.10.014 (2015). -   Gorman, J. et al. Structures of HIV-1 Env V1V2 with broadly     neutralizing antibodies reveal commonalities that enable vaccine     design. Nature structural & molecular biology 23, 81-90,     doi:10.1038/nsmb.3144 (2016). -   11 Liao, H. X. et al. Co-evolution of a broadly neutralizing HIV-1     antibody and founder virus. Nature 496, 469-476,     doi:10.1038/nature12053 (2013). -   12 Bonsignori, M. et al. Maturation Pathway from Germline to Broad     HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell 165, 449-463,     doi:10.1016/j.cell.2016.02.022 (2016). -   13 Dal Porto, J. M., Haberman, A. M., Kelsoe, G. & Shlomchik, M. J.     Very low affinity B cells form germinal centers, become memory B     cells, and participate in secondary immune responses when higher     affinity competition is reduced. The Journal of experimental     medicine 195, 1215-1221 (2002). -   14 Shih, T. A., Meffre, E., Roederer, M. & Nussenzweig, M. C. Role     of BCR affinity in T cell dependent antibody responses in vivo.     Nature immunology 3, 570-575, doi:10.1038/ni803 (2002). -   McGuire, A. T. et al. Specifically modified Env immunogens activate     B-cell precursors of broadly neutralizing HIV-1 antibodies in     transgenic mice. Nature communications 7, 10618,     doi:10.1038/ncomms10618 (2016). -   16 Jardine, J. G. et al. HIV-1 broadly neutralizing antibody     precursor B cells revealed by germline-targeting immunogen. Science     351, 1458-1463, doi:10.1126/science.aad9195(2016). -   17 Sanders, R. W. et al. HIV-1 VACCINES. HIV-1 neutralizing     antibodies induced by native-like envelope trimers. Science 349,     aac4223, doi:10.1126/science.aac4223 (2015). -   18 Bradley, T. et al. Structural Constraints of Vaccine-Induced     Tier-2 Autologous HIV Neutralizing Antibodies Targeting the     Receptor-Binding Site. Cell reports 14, 43-54,     doi:10.1016/j.celrep.2015.12.017 (2016).

Example 6A: Vaccine Antigen Design Based on the Evolution of Breadth of the CH235 bNAb Lineage

Four CH505 Vaccine Candidates Based on the Evolution of Breadth of the CH235 Lineage, Targeting the CD4bs

The mutant called CH505.M5 is the starting point for identifying CH505 vaccine candidates. CH505.M5 is one amino acid different than the CH505 TF strain, with a single N279K change, that occurred very early and conferred resistance to the cooperating CH103 lineages.

Identification of Signature Sites in the Contact Surface of the Antibody (<8.5 A)

Mutational patterns in the signature sites in the contact surface of the antibody are determined (in the global Tier II panel, as well as in our subjects). These sites are related to heterologous and autologous neutralization sensitivity/resistance signatures. The pattern of critical interest is the set of mutations (in this case, 6 positions with mutations that are common in the circulating population) that were associated with a high degree of resistance in the heterologous population to early CH235 lineage members, but that were less restrictive for late lineage members. These amino acids were also associated with a high degree of resistance to early antibodies among CH505's Envs, and so escape in the autologous population. Later lineage members acquired the ability to recognize these mutations, presumably due to the selection imposed by exposure to the resistance mutations in vivo. These late antibodies then had expanded breadth at the population level, presumably due to selection for recognition of these mutations.

These amino acids are not associated with the best binding of the antibodies at intermediate steps (earlier hypotheses for selecting Envs was to simply pick those that bound best to intermediate linage members). As the increase in breadth in the heterologous panel coincides with a gained capacity to recognize resistance mutations, Envs are picked based on their potential to expand Ab recognition to tolerate common resistance mutations and also to require Envs that had at least some capacity to bind to lineage members, but placing emphasis on covering common signatures, not on highest binders.

Hypervariable V5 region length was also a strong signature for recognition, and early lineage members could only see short V5's. Longer V5s were selected by the early antibodies, and later antibodies could recognize viruses with longer V5s, which are more representative of the heterologous population.

The mutations conferring viral escape (or relative resistance) from early lineage antibodies are educating the later antibodies.

Later antibodies in the lineage gain breadth at the population level because they evolved the capacity to recognize particular resistance conferring amino acids that arose in vivo.

Envs that are associated with jump in breadth from the UCA→CH235→CH235.9→CH235.12 are defined. The amino acids that are statistically most closely associated with distinct increases in breadth, the heterologous signatures, are identified. These signatures are related back to cycles of escape/recognition in vivo—exposure to these signature amino acids seems to trigger the increase breadth. FIG. 35 shows the heterologous panel heatmap of IC50s for CH235UCA, CH235, CH235.9, CH235.12, and VRC01 for 202 Envs.

Mutations that are common in the circulating population and are heterologous signatures are shown on the right of FIG. 36. The 207 M group panel is grouped by bNAb sensitivity—antibodies marked with an asterisk are sensitive. Selected based only on CH235 lineage signatures at the population level, the env mutations in subject CH505 are shown in the left of FIG. 36. These contact signature amino acids are enriched among viruses that are resistance to CH235 and and CH235.9, and sensitive to CH235.12.

Envs from CH505 that carried the signature mutations were picked, requiring at least some binding of later antibodies to the antigens and that they carried modest increases in V5 length relative to M5 (FIG. 38). M5 was the best trigger for CH235 like antibodies. Env30.25 gave a gentle nudge towards the most common mutations at the population level, where CH505 TF differed from consensus. An increase in V5 length is present. Env53.25 increase the V5 length, and adds three other relatively common mutations. Env 53.29 adds 471E, that may inhibit CH235.9 binding, but CH235.12 can recognized viruses with 471E. None of the CH235 Envs tested with the E275K mutation bound any of the CH235 lineages, they were not included in the set. As there is no binding data, T278S comes up too late be included in the set.

Although CH235.12 binds Envs that carry K97E and G471E with low affinity, the differential capacity to recognize heterologous Envs between CH235.9 and CH235.12 is very strongly associated with CH235.12's ability to recognize Envs that have an E in either one of those 2 positions, so including them here may enable selection of antibodies that can recognize these quite common mutations at the population level, that restrict CH235's early lineage member's breadth (FIG. 39).

A main difference between the choice of CH505 immunogens in FIG. 40 (Selection F) and Selection G is in signature position 97 and 471. These are invariant among these six strains, with K97 and G471. But each has an E among the antigens selected on FIG. 38.

Example 7: Animal Studies

The immunogens of the invention, for example Selection F (M5, M11, 20.14, 30.20, 30.12, 136.B18) could be tested in any suitable non-human animal model. Immune responses, including B cell and T cell responses to the vaccine, could be measured by any suitable assay and criteria, such as but non limited plasma neutralization, plasma binding to vaccine and/or heterologous envelopes and/or viruses could be measured. Animals studies with various forms of the selected immunogens are contemplated: gp160 mRNA of M5, M11, 20.14, 30.20, 30.12, 136.B18 (NHP #141), 6-valent M5, M11, 20.14, 30.20, 30.12, 136.B18 as SOSIP trimers (NHP #142), mRNA of 6-valent stabilized SOSIP trimers of M5, M11, 20.14, 30.20, 30.12, 136.B18 (NHP #140), gp145DNA of CH505M5 and CH505M11 as a prime and a subsequence boost(s), followed by 6-valent M5, M11, 20.14, 30.20, 30.12, 136.B18 SOSIP trimers (e.g. NHP #139). In some embodiments the SOSIP trimer is SOSIP v4.1. Any other trimer design is contemplated. Any suitable adjuvant could be used. Studies could be performed in any suitable animal model. Studies could be performed in adults and neonates.

TABLE 15 NHP Study #139: gp145 DNA M5 + M11(x2) + 6-valent 4.1 SOSIP in neonates. Done at Bleed Receive @ Instructions Samples receiving Date BIDMC (I.D. Immunizations) Qty/Volume Needed laboratory Wk 0 Wk 0 Bleed + Immunize neonates only: EDTA+ Freeze **Prebleed M5 gp 145 DNA (2 mg) + +Stool + Rectal plasma in Processed M11 gp 145 DNA (2 mg) swabs + saliva 250 uL at Bioqual IM +IDEXX serum aliquots chems + CBC *Bioqual to freeze Wk 0 samples Wk 2 Wk 2 Bleed all animals EDTA+ Freeze +Stool + Rectal plasma in swabs + saliva 250 uL +IDEXX serum aliquots chems + CBC Wk 4 Wk 4 Immunize neonates only: Stool + Rectal M5 gp 145 DNA (2 mg) + swabs + saliva M11 gp 145 DNA (2 mg) IM Wk 6 Wk 6 Bleed all animals EDTA+ Freeze +Stool + Rectal plasma in swabs + saliva 250 uL +IDEXX serum aliquots; all chems + CBC PBMCs Wk 8 Wk 8 Immunize neonates only: Stool + Rectal M5 SOSIP 4.1 stable trimer (25 ug) + swabs + saliva M11 SOSIP 4.1 stable trimer (25 ug) In Poly ICLC (Hiltonol) = 200 ug IM Wk 10 Wk 10 Bleed all animals EDTA+ Freeze +Stool + Rectal plasma in swabs + saliva 250 uL +IDEXX serum aliquots; all chems + CBC PBMCs Wk 12 Wk 12 Immunize neonates only: Stool + Rectal 20.14 SOSIP 4.1 stable trimer (50 ug) swabs + saliva In Poly ICLC (Hiltonol) = 200 ug IM Wk 14 Wk 14 Bleed all animals EDTA + SST Freeze serum +Stool + Rectal and plasma in swabs + saliva 250 uL +IDEXX serum aliquots; all chems + CBC PBMCs Wk 16 Wk 16 Immunize neonates only: Stool + Rectal 30.20 SOSIP 4.1 stable trimer (50 ug) swabs + saliva In Poly ICLC (Hiltonol) = 200 ug IM Wk 18 Wk 18 Bleed all animals EDTA + SST Freeze serum +Stool + Rectal and plasma in swabs + saliva 250 uL +IDEXX serum aliquots; all chems + CBC PBMCs Wk 20 Wk 20 Immunize neonates only: Stool + Rectal 30.12 SOSIP 4.1 stable trimer swabs + saliva In Poly ICLC (Hiltonol) = 200 ug IM Wk 22 Wk 22 Bleed all animals EDTA + SST Freeze serum +Stool + Rectal and plasma in swabs + saliva 250 uL +IDEXX serum aliquots chems + CBC Wk 24 Wk 24 Immunize neonates only: Stool + Rectal 136.B8 SOSIP 4.1 stable trimer swabs + saliva In Poly ICLC (Hiltonol) = 200 ug IM Wk 26 Wk 26 Bleed all animals EDTA + SST Freeze serum +Stool + Rectal and plasma in swabs + saliva 250 uL +IDEXX serum aliquots chems + CBC

TABLE 16 NHP study #140: mRNA 6-valent chimeric stabilized 4.1 trimers Bleed Receive @ Instructions Samples Done at Date BIDMC (I.D. Immunizations) Qty/Volume Needed BIDMC Pre- Pre- Pre-LN biopsy (axillary) 6 ml EDTA + 2 ml Freeze bleed bleed Pre-Bleed all animals and ship to Linh SST Plasma and Feb. 22, 2017 Feb. 23, 2017 Mach at BIDMC via Fedex priority +serum chemistry serum in overnight (IDEXX) + CBC 250 uL NHP's: (IDEXX) aliquots; all 150796, 150798, 150794, 150252 PBMC Wk 0 Wk 0 Bleed all animals and immunize: No No Feb. 28, 2017 Feb. 29, 2017 M5 chimeric stabilized trimer (kos) sampling sampling mRNA-LNP 50 ug + M11 chimeric stabilized trimer (kos) mRNA-LNP 50 ug ID = 10 sites on the back Give M5 and M11 separately at different sites to avoid heterotrimers mRNA-LNPs: *diluted in calcium and magnesium free PBS where needed. *once thawed are stored on ice and administered within 2 hours NHP's: 150796, 150798, 150794, 150252 Wk 1 Wk 1 Bleed all animals 6 ml EDTA + 2 ml Freeze Mar. 7, 2017 Mar. 8, 2017 LN biopsy (inguinal) SST Plasma and +serum chemistry serum in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMC Wk 2 Wk 2 Bleed all animals 6 ml EDTA + 2 ml Freeze Mar. 14, 2017 Mar. 15, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 4 Wk 4 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Mar. 29, 2017 Mar. 30, 2017 20.14 chimeric stabilized trimer (kos) SST serum and mRNA-LNP 50 ug +serum chemistry plasma in ID = 10 sites on the back (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 5 Wk 5 Bleed all animals 6 ml EDTA + 2 ml Freeze Apr. 5, 2017 Apr. 6, 2017 LN biopsy (inguinal) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 6 Wk 6 Bleed all animals 6 ml EDTA + 2 ml Freeze Apr. 12, 2017 Apr. 13, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 8 Wk 8 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Apr. 26, 2017 Apr. 27, 2017 30.20 chimeric stabilized trimer (kos) SST serum and mRNA-LNP 50 ug +serum chemistry plasma in ID = 10 sites on the back (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 9 Wk 9 Bleed all animals 6 ml EDTA + 2 ml Freeze May 3, 2017 May 4, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 10 Wk 10 Bleed all animals 6 ml EDTA + 2 ml Freeze May 10, 2017 May 11, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 12 Wk 12 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze May 24, 2017 May 25, 2017 30.12 chimeric stabilized trimer (kos) SST serum and mRNA-LNP 50 ug +serum chemistry plasma in ID = 10 sites on the back (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 13 Wk 13 Bleed all animals 6 ml EDTA + 2 ml Freeze May 31, 2017 Jun. 1, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 14 Wk 14 Bleed all animals 6 ml EDTA + 2 ml Freeze Jun. 7, 2017 Jun. 8, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 16 Wk 16 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Jun. 21, 2017 Jun. 22, 2017 136.B18 chimeric stabilized trimer (kos) SST serum and mRNA-LNP 50 ug +serum chemistry plasma in ID = 10 sites on the back (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 17 Wk 17 Bleed all animals 6 ml EDTA + 2 ml Freeze Jun. 28, 2017 Jun. 29, 2017 LN biopsy (axillary) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 18 Wk 18 Bleed all animals 6 ml EDTA + 2 ml Freeze Jul. 5, 2017 Jul. 6, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 20 Wk 20 Bleed all animals 6 ml EDTA + 2 ml Freeze Jul. 19, 2017 Jul. 20, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 24 Wk 24 Bleed all animals 6 ml EDTA + 2 ml Freeze Aug. 2, 2017 Aug. 3, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 28 Wk 28 Bleed all animals 6 ml EDTA + 2 ml Freeze Aug. 16, 2017 Aug. 17, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs

The mRNA immunogens are delivered by a lipid nanoparticle (LNP) technology. The LNPs comprises four different lipids that could self assemble to 80-100 nm size particles.

TABLE 17 NHP Study #141: mRNA 6-valent gp 160 membrane bound trimers Done at Bleed Receive @ Instructions Samples receiving Date BIDMC (I.D. Immunizations) Qty/Volume Needed laboratory Wk 0 Wk 0 Pre-LN biopsy (axillary) Pre-LN biopsy Freeze serum Nov. 9, 2016 Nov. 10, 2016 Immunize all 4 animals: (axillary and plasma 4 NHPs (4 NOTchallenged monkeys 4 ml EDTA + 2 ml in 250 uL from #129 vaccinated): SST aliquots 6858(M), 150250(F), 150793(M), 150795(M) M5 gp 160 membrane bound trimer mRNA-LNP 50 ug + M11 gp 160 membrane bound trimer mRNA-LNP 50 ug ID = 60 ul × 10 sites on the back Give M5 and M11 separately at different sites to avoid heterotrimers mRNA-LNPs: *diluted in calcium and magnesium free PBS where needed. *once thawed are stored on ice and administered within 2 hours Wk 1 Wk 1 Bleed all animals + Draining lymph 2 ml EDTA + Freeze Nov. 16, 2016 Nov. 17, 2016 node biopsies (axillary) Draining lymph plasma in node biopsies 250 uL (axillary) aliquots Wk 2 Wk 2 Bleed all animals 6 ml EDTA + 2 ml Freeze serum Nov. 21, 2016 Nov. 22, 2016 SST and plasma in 250 uL aliquots; all PBMCs Wk 4 Wk 4 Bleed all animals and immunize: 4 ml EDTA + 2 ml Freeze serum Dec. 6, 2016 Dec. 7, 2016 20.14 gp 160 membrane bound trimer SST and plasma mRNA-LNP 50 ug in 250 uL ID = 60 ul × 10 sites on the back aliquots Wk 5 Wk 5 Bleed all animals + Draining lymph 3 ml EDTA + Freeze serum Dec. 13, 2016 Dec. 14, 2016 node biopsies (inguinal) Draining lymph and plasma node biopsies in 250 uL (inguinal) aliquots; all PBMCs Wk 6 Wk 6 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Dec. 20, 2016 Dec. 21, 2016 SST and plasma in 250 uL aliquots; all PBMCs Wk 7 Wk 7 Bleed all animals 3 ml EDTA Freeze Dec. 27, 2016 Dec. 28, 2016 plasma in 250 uL aliquots; all PBMCs Wk 8 Wk 8 Bleed all animals and immunize: 4 ml EDTA + 2 ml Freeze serum Jan. 4, 2017 Jan. 5, 2017 30.20 gp 160 membrane bound trimer SST and plasma mRNA-LNP 50 ug in 250 uL ID = 60 ul × 10 sites on the back aliquots Wk 9 Wk 9 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Jan. 11, 2017 Jan. 12, 2017 SST and plasma in 250 uL aliquots Wk 10 Wk 10 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Jan. 18, 2017 Jan. 19, 2017 SST and plasma in 250 uL aliquots; all PBMCs Wk 12 Wk 12 Bleed all animals and immunize: 4 ml EDTA + 2 ml Freeze serum Jan. 31, 2017 Feb. 1, 2017 30.12 gp 160 membrane bound trimer SST and plasma mRNA-LNP 50 ug in 250 uL ID = 60 ul × 10 sites on the back aliquots Wk 13 Wk 13 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Feb. 8, 2017 Feb. 9, 2017 SST and plasma in 250 uL aliquots; all PBMCs Wk 14 Wk 14 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Feb. 14, 2017 Feb. 15, 2017 SST and plasma in 250 uL aliquots; all PBMCs Wk 16 Wk 16 Bleed all animals and immunize: 4 ml EDTA + 2 ml Freeze serum Feb. 28, 2017 Mar. 1, 2017 136.B18 gp 160 membrane bound SST and plasma trimer mRNA-LNP 50 ug in 250 uL ID = 60 ul × 10 sites on the back aliquots Wk 17 Wk 17 Bleed all animals + Draining lymph 3 ml EDTA + 1 ml Freeze serum Mar. 7, 2017 Mar. 8, 2017 node biopsies (inguinal) SST + Draining and plasma lymph node in 250 uL biopsies (inguinal) aliquots; all PBMCs Wk 18 Wk 18 Bleed all animals 3 ml EDTA + 2 ml Freeze serum Mar. 14, 2017 Mar. 15, 2017 SST and plasma in 250 uL aliquots; all PBMCs Wk 20 Wk 20 Bleed all animals 4 ml EDTA + 2 ml Freeze serum Mar. 28, 2017 Mar. 29, 2017 SST and plasma in 250 uL aliquots Wk 24 Wk 24 Bleed all animals 4 ml EDTA + 2 ml Freeze serum Apr. 25, 2017 Apr. 26, 2017 SST and plasma in 250 uL aliquots Wk 28 Wk 28 Bleed all animals 4 ml EDTA + 2 ml Freeze serum May 23, 2017 May 24, 2017 SST and plasma in 250 uL aliquots

TABLE 18 NHP Study #142: 6-valent chimeric stabilized trimer protein (kos) Bleed Receive @ Instructions Samples Done at Date BIDMC (I.D. Immunizations) Qty/Volume Needed BIDMC Feb. 22, 2017 Feb. 23, 2017 Pre-LN biopsy (axillary) 6 ml EDTA + 2 ml Freeze Pre-Bleed all animals and ship to Linh SST serum and Mach at BIDMC via Fedex priority +serum chemistry plasma in overnight (IDEXX) + CBC 250 uL NHP's: (IDEXX) aliquots; all 150251, 6857, T244, T245 PBMCs Wk 0 Wk 0 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Feb. 28, 2017 Feb. 29, 2017 NHP #: SST serum and 150251, 6857, T244, T245 +serum chemistry plasma in M5 chimeric stabilized trimer (kos) + (IDEXX) + CBC 250 uL M11 chimeric stabilized trimer (kos) (IDEXX) aliquots; all IM injections PBMCs Wk 1 Wk 1 Bleed all animals 6 ml EDTA + 2 ml Freeze Mar. 7, 2017 Mar. 8, 2017 LN biopsy (inguinal) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 2 Wk 2 Bleed all animals 6 ml EDTA + 2 ml Freeze Mar. 14, 2017 Mar. 15, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 4 Wk 4 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Mar. 29, 2017 Mar. 30, 2017 20.14 chimeric stabilized trimer (kos) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 5 Wk 5 Bleed all animals 6 ml EDTA + 2 ml Freeze Apr. 5, 2017 Apr. 6, 2017 LN biopsy (inguinal) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 6 Wk 6 Bleed all animals 6 ml EDTA + 2 ml Freeze Apr. 12, 2017 Apr. 13, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 8 Wk 8 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Apr. 26, 2017 Apr. 27, 2017 30.20 chimeric stabilized trimer (kos) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 9 Wk 9 Bleed all animals 6 ml EDTA + 2 ml Freeze May 3, 2017 May 4, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 10 Wk 10 Bleed all animals 6 ml EDTA + 2 ml Freeze May 10, 2017 May 11, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX)) aliquots; all PBMCs Wk 12 Wk 12 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze May 24, 2017 May 25, 2017 30.12 chimeric stabilized trimer (kos) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 13 Wk 13 Bleed all animals 6 ml EDTA + 2 ml Freeze May 31, 2017 Jun. 1, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 14 Wk 14 Bleed all animals 6 ml EDTA + 2 ml Freeze Jun. 7, 2017 Jun. 8, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 16 Wk 16 Bleed all animals and immunize: 6 ml EDTA + 2 ml Freeze Jun. 21, 2017 Jun. 22, 2017 136.B18 chimeric stabilized trimer SST serum and (kos) +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 17 Wk 17 Bleed all animals 6 ml EDTA + 2 ml Freeze Jun. 28, 2017 Jun. 29, 2017 LN biopsy (axillary) SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs Wk 18 Wk 18 Bleed all animals 6 ml EDTA + 2 ml Freeze Jul. 5, 2017 Jul. 6, 2017 SST serum and +serum chemistry plasma in (IDEXX) + CBC 250 uL (IDEXX) aliquots; all PBMCs

This protocol describes NHP immunization study with M5, M11, 20.14, 30.20, 30.12, 136.B18 envelopes and SIVGag. In some embodiments the below vaccination regimen could be carried out with the proteins delivered as trimers, for example but not limited to SOSIP.III trimers.

TABLE 19 Samples Bleed Date Instructions Qty/Volume Needed Notes Pre (−12 Collect pre samples Plasma, PBMC, serum, to −4 weeks) (−12 to −4 weeks) saliva, rectal swab, vaginal swab, LN (axillary) Wk 0 Vaccination #1: M5 + M11 Plasma, PBMC, serum, (EP1) Vaccine HIV env gp 145 DNA & SIV gag saliva, rectal swab, vaginal DNA (Conserved element CE prime swab, fecal sample followed by C0-delivery of CE & complete gag boost) DNA dose = 2 mg of each construct Protein HIV gp 120. Env dose = 200 ug of each protein Adjuvant = GLA-SE 25 ug Route: IM/EP Innovio (n = 5) Group 1A Group 1B Group 1C Group 1D DNA + Protein co-immunization (both sides) = into same muscle Group 2A Group 2B Group 2C Group 2D DNA (Left side) + Protein (Right side) = separate sides and muscles Group 3A Group 3B Sham DNA and adjuvant co-immunization (Both Sides) = same muscle Group 4A Group 4B Treatment naive Wk 1 LN G3A, G3B, G4A, G4B @ Lt only Plasma, PBMC, serum (EP1wk 1) Wk 2 Plasma, PBMC, serum, (EP1 Wk 2) saliva, rectal swab, vaginal swab, fecal sample Wk 8 Vaccination #2: 20.14 Plasma, PBMC, serum (EP2) DNA dose = 2 mg of each construct Env dose = 200 ug of each protein Wk 9 LN ing G1A, G2A @ Rt & Lt Plasma, PBMC, serum (EP2 wk 1) LN G3A, G3B, G4A, G4B @ Rt only Wk 10 BM G1A, G2A Plasma, PBMC, serum, (EP2 wk 2) saliva, rectal swab, vaginal swab, fecal sample, vaginal bx, rectal bx Wk 16 Plasma, PBMC, serum Wk 24 Vaccination #3: 30.20 Plasma, PBMC, serum (EP3) DNA dose = 2 mg of each construct Env dose = 200 ug of each protein Wk 25 LN ing G1B, G2B Rt & Lt Plasma, PBMC, serum, (EP3 wk 1) Wk 26 BM G1B, G2B Plasma, PBMC, serum, (EP3 wk 2) saliva, rectal swab, vaginal swab, fecal sample Wk 32 Plasma, PBMC Wk 40 Vaccination #4: 30.12 Plasma, PBMC, serum (EP 4) DNA dose = 2 mg of each construct Env dose = 200 ug of each protein Wk 41 LN ing G1C, G2C Rt & Lt Plasma, PBMC, serum (EP 4 wk 1) Wk 42 BM G1C, G2C Plasma, PBMC, serum, (EP4 wk 2) saliva, rectal swab, vaginal swab, fecal sample, vaginal bx, rectal bx Wk 48 Plasma, PBMC Wk 56 Vaccination #5: 136.B18 Plasma, PBMC, serum (EP5) DNA dose = 2 mg of each construct Env dose = 200 ug of each protein Wk 57 LN ing G1D, G2D Rt & Lt Plasma, PBMC, serum (EP5 wk 1) Wk 58 BM G1D, G2D Plasma, PBMC, serum, (EP5 wk 2) *Necropsy 2 animals saliva, rectal swab, vaginal swab, fecal sample Wk 64 Plasma, PBMC Wk 74 Plasma, PBMC, serum, saliva, rectal swab, vaginal swab, fecal sample

Non-limiting example of an immunization protocols with Selection F (M5, M11, 20.14, 30.20, 30.12, 136.B18). In this example the immunogens are delivered as mRNA formulated in nanoparticles. In some embodiments the stabilized trimers are of the design SOSIP.III.

Materials needed: Formulate mRNA for 6 monkeys. 6 doses×50 ug/nhp=300 ug of each mRNA construct.

Collections of Plasma, Serum, and PBMC: Collect all plasma and serum in 250 uL aliquots and save all PBMCs. CBC collection: 850 uL from each animal

Animal studies using the above protocols could be carried out with the immunogens of Selection G (EnvSeq-2), or Selection H (EnvSeq-3).

Animal studies with envelopes CH505 T/F, as stable trimers are also contemplated. Non-limiting examples of such studies include: CH505 T/F as gp145 nucleic acid prime (once or twice), followed by sequential SOSIP 4.1 trimers of CH505 T/F, CH505 w53.16, CH505 w78.33, CH505 w100.B6. In some embodiments there is no nucleic acid prime and immunization regimen comprises sequential SOSIP 4.1 trimers of CH505 T/F, CH505 w53.16, CH505 w78.33, CH505 w100.B6. In some embodiments the nucleic acid is mRNA. In some embodiments the nucleic acid is DNA. In some embodiments the DNA is administered via electroporation. In some embodiments of these studies, animals could be boosted with CH505 w136.B8.

Example 8: Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody

Antibodies with ontogenies from V_(H)1-2 or V_(H)1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here we define with longitudinal sampling from time-of-infection the development of a V_(H)1-46-derived antibody lineage that matured to neutralize 90% of HIV-1 isolates. Structures of lineage antibodies CH235 (week 41 from time-of-infection, 18% breadth), CH235.9 (week 152, 77%) and CH235.12 (week 323, 90%) demonstrated the maturing epitope to focus on the conformationally invariant portion of the CD4bs. Similarities between CH235 lineage and five unrelated CD4bs lineages in epitope focusing, length-of-time to develop breadth, and extraordinary levels of somatic hypermutation suggested commonalities in maturation among all CD4bs antibodies. Fortunately, the required CH235-lineage hypermutation appeared substantially guided by the intrinsic mutability of the V_(H)1-46 gene, which closely resembled V_(H)1-2. We integrated our CH235-lineage findings with a second broadly neutralizing lineage and HIV-1 co-evolution to suggest a vaccination strategy for inducing both lineages.

Introduction

Understanding the pathways and mechanisms of broadly neutralizing antibody (bnAb) induction is a critical goal of HIV-1 vaccine development (Bonsignori et al., 2012; Haynes, 2015; Haynes and Bradley, 2015; Haynes et al., 2012; Mascola and Haynes, 2013;). In chronic HIV-1 infections, breadth of plasma neutralization follows a uniform distribution and broad neutralization arises in ˜50% of individuals after 5 years or more of infection (Hraber et al., 2014). The delayed appearance of bnAbs suggests roadblocks to their development, and one vaccine approach is to decipher these roadblocks and devise strategies to overcome them. It is possible that—because of the high diversity of antibodies resulting from recombination and somatic hypermutation (SHM)—different bnAb lineages may have different developmental pathways and roadblocks. However, for the CD4-binding site (CD4bs), a population-level analysis on 14 donors indicated only two general types of CD4bs bnAbs: V_(H)-gene restricted and CDR H3-dominated (Zhou et al., 2015).

The V_(H)-gene restricted classes arise from two highly similar V_(H)-genes: V_(H)1-2 and V_(H)1-46 (Scheid et al., 2011; Wu et al., 2011). V_(H)1-2*02 and V_(H)1-46*01 share 93.4% (269/288) nucleotide sequence identity. Both classes give rise to antibodies that recognize the CD4bs via V_(H) structural mimicry of the immunoglobulin-like N-terminal domain of CD4 (Zhou et al., 2010; Zhou et al., 2015). For the V_(H)1-2 gene-derived antibodies, analysis of their ontogeny suggests two roadblocks based on: (i) a requirement for high levels of SHM (Klein et al., 2013; Scheid et al., 2009; Scheid et al., 2011; Wu et al., 2010), and (ii) weak binding of the inferred unmutated common ancestor (UCA) to gp120 (Jardine et al., 2013; McGuire et al., 2013; Scheid et al., 2011; Wu et al., 2011; Zhou et al., 2010; Zhou et al., 2015), although a definitive analysis from time-of-infection had not yet provided detail. In addition, several of the CD4bs bnAbs are autoreactive with ubiquitinase enzymes (Bonsignori et al., 2014; Liao et al., 2013; Liu et al., 2015).

Structure-based design of UCA-interacting immunogens has recently demonstrated a means to overcome this second roadblock, with priming of V_(H)1-2 bnAb lineages in knock-in mice (Dosenovic et al., 2015; Jardine et al., 2015). However, the maturation of primed V_(H)1-2 CD4bs B cell lineages to broad neutralization as well as the mechanism for the development of breadth remain unresolved.

For the V_(H)1-46-derived antibodies, far less is known. Two chronically HIV-infected individuals, RU1 and RU8, have developed V_(H)1-46-derived bnAbs, 1B2530 and 8ANC131 (Scheid et al., 2011). We recently described an African individual (donor CH505) who, over time, developed a CD4bs bnAb lineage (the CH103 lineage) that recognized the CD4 supersite through a CDR H3-dominated mode of interaction (Liao et al., 2013). Analysis of the co-evolution between virus and CH103 lineage demonstrated a second B cell lineage (the CH235 lineage) that cooperated by selection of escape mutants from the CH235 lineage that drove the CH103 bnAb lineage (Gao et al., 2014). Here we find that the CH235 lineage itself progressed to bnAb over 5 years of affinity maturation. We identify sequences of the CH235 lineage through longitudinal samples of 17 time points spanning weeks (wks) 6-323 post infection, assess neutralization breadth of sequential lineage members on a panel of ˜200 diverse isolates, and determine Env-complexed crystal and EM structures for lineage members. We analyze the conformity (i.e. the level of shared mutation positions and identical sequence mutations) of CH235 lineage development relative to other V_(H) gene-specific bnAb lineages in other donors, as well as the co-evolution of virus and CH235 lineage. Despite an early near-optimal binding orientation, the CH235 lineage required over 20% SHM to reach 90% neutralization breadth. Our results provide insight into the difficulties in focusing recognition to the conserved site of HIV-1 vulnerability, and suggest that CD4bs-directed antibodies, whether V_(H)-gene restricted or CDR H3-dominated, face similar obstacles in development. For V_(H)1-46- and V_(H)1-2-derived CD4-mimic antibodies, the unique genetic mutability inherent in each of these two V_(H)-germline genes helps to direct maturation, potentially providing an explanation for the prevalence of effective CD4bs antibodies derived from these two germline genes.

Results

Sequencing of B Cell Antibody Gene Rearrangements in Longitudinal Samples.

To understand the maturation of the cooperating CH235 lineage in donor CH505, we sought to identify sequences of lineage members at 17 time points, spanning wks 6 to 323 from time of infection. We first asked when we could detect members of the CH235 lineage. Next-generation sequencing (NGS) of antibody heavy chain gene rearrangements amplified from genomic DNA template of blood mononuclear cells from wk 6 to 152 (15 time points) identified a total of 479,028 unique, non-duplicated V-heavy sequences. The first V-heavy sequences belonging to the CH235 B cell lineage were found at wk 14, and additional CH235 lineage members were found at all subsequent time points. Only unique sequences in the CH235 lineage were further investigated and they were assigned to the earliest time-point (time-of-appearance) in which they were identified. Four V-heavy sequences were paired with the closest V_(L) from isolated antibodies and produced as recombinant monoclonal antibodies (mAbs) (CH235.6 through CH235.9). From cultured memory B cells collected 41 wks post-transmission we had previously isolated five members of the CH235 lineage (CH235, CH236, CH239, CH240 and CH241) (Gao et al., 2014) and we have now isolated four additional members with natural V_(H) and V_(L) pairing from cultured memory B cells collected at wks 264 and 323 post-transmission: CH235.10 through CH235.13 (FIG. 41A, FIG. 48A and FIG. 53). CH235 lineage antibodies represented 0.018% of the total memory B cell repertoire and 0.5% of the CH505 TF gp120-specific memory B cell population.

The CH235 lineage could be separated into three clades (clade I, II and III). Clade I showed a number of early lineage members, but no additional clade I sequences were observed after wk 30; clade II showed further development and included members CH241 (wk 41) and CH235.6 (wk 66), but no additional sequences were observed after wk 66; clade III developed through wk 323 and included antibodies CH235 (wk 41), CH235.9 (wk 152), and CH235.12 (wk 323) (FIG. 41A).

CH235 Lineage HIV-1 Neutralization.

To characterize the development of neutralization breadth in the CH235 lineage, we assessed antibodies in clade III for their ability to neutralize diverse HIV-1 isolates in a 199-isolate panel (FIG. 41B and FIG. 54). No isolates were neutralized by the unmutated common ancestor (UCA), whereas 18% of the viruses were neutralized by CH235 at wk 41. By wk 152, CH235.9 neutralized 77% of viruses, although with a relatively weak potency of 3 μg/ml. By wk 323, however, CH235.12 was able to neutralize 90% of viruses, and the neutralization 50% inhibitory concentration (IC₅₀) potency increased by 5-fold to 0.6 μg/ml.

We next analyzed the heterologous neutralization pattern of these antibodies to understand their development of broad neutralization (FIG. 48B) (Georgiev et al., 2013). CH235 lineage members and previously identified HIV-1 bnAbs were clustered based on heterologous neutralization activity. CH235 neutralization activity was more similar to CD4bs bnAbs than to bnAbs with other epitope specificities. While the CH235 neutralization profile was the most divergent from other CD4bs bnAbs, CH235.9 and CH235.12 were much more similar to other CD4bs bnAbs and each other. Interestingly, despite V_(H)1-46 usage, the CH235.9 and CH235.12 neutralizing profile was more similar to that of V_(H)1-2-derived antibodies, such as VRC01, than V_(H)1-46-derived antibodies, such as 8ANC131 (FIG. 48B).

Crystal Structures of CH235-Lineage Members with HIV-1 gp120.

To provide structural insight into the recognition and maturation of the CH235 lineage, we prepared the antigen-binding fragments (Fabs) of antibodies CH235 (wk 41 from time of infection, 18% breadth), CH235.9 (wk 152, 77%) and CH235.12 (wk 323, 90%), and co-crystallized, solved and refined these in complex with the gp120 core of HIV-1 isolate strain (93TH057) (FIGS. 42A-E, FIG. 55). We mapped the location of residues altered during SHM and observed changes throughout the variable domain (FIG. 42A).

Comparison of the orientation of the V_(H) of CH235 in Env binding with that of CD4, VRC01 and 8ANC131 (Scheid et al., 2011) showed that the CH235 V_(H) domain mimicked CD4 in Env binding and was highly similar to the V_(H) orientation and structure of the VRC01 and 8ANC131 V_(H) chains: in particular, the V_(H)1-46 of CH235 preserved key contacts mediated by the CDR H2 loop for the CD4 binding loop and for the gp120 D368 (FIG. 49A,B).

Analysis of the angle of recognition for the CH235 lineage indicated little change during maturation, with CH235, CH235.9 and CH235.12 all clustering within the larger VRC01-class of antibodies. Interestingly, other V_(H)1-46 antibodies clustered differently, with antibody 1B2530 from HIV-1-positive donor RU1 at a highly similar angle and 1.5 Å translated, and antibodies 8ANC131 and 8ANC134 from HIV-1-positive donor RU8 occupying a cluster about 55 degrees and 3.5 Å translated related to the CD4 (FIG. 49C).

These results suggest that the gp120-antibody orientation was determined early in bnAb lineage ontogeny, with further maturation maintaining the same general orientation. Overall, the structures of CH235 lineage members with HIV-1 gp120 Env revealed CD4 mimicry. While the V_(H) gene usage classifies the CH235 lineage within the V_(H)1-46-derived 8ANC131 bnAb class, it is both functionally and structurally closer to the VRC01 class (Zhou et al., 2015).

Negative Stain EM of CH235-Lineage Members with Trimeric HIV-1 Env.

To visualize the recognition of the CH235 lineage in the context of the HIV-1 Env trimer, we used negative stain EM to determine 3D-reconstructions of Fabs CH235, CH235.9 and CH235.12 bound to trimeric BG505 and B41 HIV-1 Env glycoproteins (FIG. 42B)(Pugach et al., 2015; Sanders et al., 2013). Notably, the stoichiometry increased with antibody maturation, with CH235 (8% V_(H) mutation) binding with a stoichiometry of 1:1 (BG505; FIG. 42B, top, FIG. 49D-F) or 2:1 (B41; FIG. 42B, bottom, FIG. 49D-F) Fabs per trimer and CH235.9 and CH235.12 (19% and 25% V_(H) mutation, respectively) binding with a 3:1 Fab to trimer ratio (FIG. 42B). We next compared the orientation and stoichiometry of CH235.12 Fab with that of CH103, a CDR H3-dependent CD4bs bnAb isolated from the same subject (Liao et al., 2013). EM analysis of either CH235.12 or CH103 Fab in complex with BG505 SOSIP.664 revealed structural differences between the CDR H3-dominated CH103 class bnAb and the 8ANC131-class CH235.12 bnAb and, in accordance with crystallographic results, the angle of approach of CH235 was similar to that of VRC01 and other CD4 mimicking bnAbs (FIG. 49G).

Despite the CD4 mimicry by CH235, the trimer remained in a closed conformation when the CH235 lineage members were bound. However, the EM-derived model of CH103 in complex with BG505 revealed that CH103 either bound to or induced a more open version of the trimer. This conformation represents an intermediate state between the closed, compact trimer in complex with CH235 or VRC01, and the CD4-induced open model in complex with soluble CD4 or 17b Fab (FIG. 49G). Similar to more mature CH235 lineage bnAb Fabs, bnAb CH103 bound to BG505 with a stoichiometry of 3 Fabs per trimer. (FIG. 49G).

Maturation Focuses CH235 Lineage Recognition to a Conserved Site of CD4 Vulnerability.

To gain insight into the structural consequences of maturation, we mapped the epitope of CH235 lineage members relative to the conformationally invariant CD4 supersite of vulnerability (Zhou et al., 2015). When we mapped the CH235 footprint on gp120, we observed portions of the CH235-binding surface on gp120 to be outside of the CD4 supersite of vulnerability (FIG. 42C, left). This surface was reduced in CH235.9 and CH235.12 structures, especially on variable loop V5. Recognition by the CH235.12 antibody concentrated almost entirely on the CD4 supersite of vulnerability, with little interactions with the inner domain or variable loop V5; there was, however, a large remaining interaction with the conserved loop D region (FIG. 42C, middle and right).

To quantify targeting precision, we computed the buried surface between antibodies and gp120 co-crystal complexes, for the region overlapping the CD4 supersite of vulnerability minus the region outside the vulnerable site. Overall targeting precision correlated with neutralization breadth (P=0.0007) (FIG. 42D). The CH235-lineage antibodies all showed good targeting precision. We also analyzed the correlation of SHM versus neutralization breadth (P=0.0097) (FIG. 42E): While the CH235 lineage generally trended towards lower SHM relative to neutralization breadth, all CD4bs bnAbs appeared to require a high degree of SHM, independent of whether the antibody derived from a specific V_(H)-gene or used a CDR H3-dominated mode of recognition.

Overall, the results suggest that maturation requires a high degree of SHM to focus recognition onto the CD4 supersite of vulnerability and that this high degree of SHM is a general requirement of all CD4bs bnAb lineages, even those that begin with highly favorable orientations such as CH235.

Conformity of Sequence Evolution of CH235 Lineage.

The mutation levels of CH235-lineage antibodies isolated 41 wks post infection from memory B cell cultures was markedly lower (range 7-11%;) than that of all previously reported V_(H)1-46 and V_(H)1-2 CD4bs bnAbs (>25%) (Scheid et al., 2011; Sui et al., 2010; Wu et al., 2010; Zhou et al., 2015) (FIG. 53). The mutation levels of CH235-lineage antibodies isolated up to 264 wks post infection increased to 20%, but were still lower than those of most other bnAbs until 323 wks post infection (CH235.12: 26% mutations) (FIG. 43A).

To quantify the conformity of CH235-lineage antibodies to the two V_(H)1-46-derived bnAbs (1B2530 from donor RU1 and 8ANC131 from donor RU8) (Scheid et al., 2011; Zhou et al., 2015), we analyzed the similarity of shared mutation positions (positional conformity) and shared identical mutations (identity conformity) of the V_(H) genes (FIG. 43B, FIG. 50A). As a comparison, we also calculated the positional conformity and identity conformity of non-HIV-1 targeting antibodies isolated from 3 HIV-1 negative donors relative to template antibodies 1B2530 and 8ANC131. Positional conformity in SHM was spread over a large range (50-90%), and there did not seem to be much discrimination between V_(H)1-46 in antibodies that effectively neutralized HIV-1 and those that did not (FIG. 43B, top panels). Identity conformity in SHM was also spread over a large range (0-75%) (FIG. 43B, bottom panels), and while little discrimination was observed between V_(H)1-46 in antibodies that effectively neutralized HIV-1 and those that did not for antibody 8ANC131, there was discrimination among CD4bs antibodies when 1B2530 was used as a reference (FIG. 43B, bottom left panel). The differences in CH235-lineage identify conformity to 1B2530 or to 8ANC131 may reflect the greater similarity of the recognition orientation of CH235-lineage members with 1B2530 (FIG. 49C) and suggested that slight differences in recognition orientation can substantially alter factors associated with identity conformity.

Overall, these results indicated SHM in response to HIV-1 infection to proceed in a manner that depended less on functional selection and more on intrinsic properties of the V_(H)1-46-gene, especially related to the position of residues that undergo SHM. To investigate further the contribution of the V_(H)1-46 gene, we analyzed SHM observed in V_(H)1-46 gene transcripts from three uninfected individuals (FIG. 43C, top); notably, all 11 positions mutated in CH235, 1B2530 and 8ANC131 were also mutated among non-HIV-1 neutralizing antibodies with high frequency (≥20%). Moreover, the residue substitutions in CH235 were frequently found in the top three most commonly observed substitutions for that position in the V_(H)1-46 gene. To quantify the impact of gene mutability, we compared the difference in probability distributions of positional and identity conformity for sequences simulated with and without taking into account the intrinsic V_(H)1-46 gene mutability. The simulations showed that both positional and identity conformity shifted to a higher level of similarity when considering gene mutability (FIGS. 50B and 50C). Notably, a substantial shift in probability was observed for the positional conformity of CH235 (FIG. 50B, FIG. 56A). Similar shifts in identity conformity were also observed for CH235 (FIG. 50C, FIG. 56B). Thus, the intrinsic susceptibility at specific sites of the V_(H)1-46 germline gene to mutation as well as to the frequency of specific mutations that existed at each of these sites appeared to be a dominant factor in the SHM alteration of the CH235 lineage. These results are in line with our previous finding that selection and mutability synergized during affinity maturation of an influenza HA-reactive clone from a non-HIV-1 infected person to hemagglutinin (HA) (Kepler et al., 2014): hence, the dominant role of intrinsic susceptibility at specific sites may be a more general biological phenomenon in dictating the course of SHM.

Because V_(H)1-2 is genetically the most closely related germline gene to V_(H)1-46, we also examined the mutability of the V_(H)1-2 gene (FIG. 43C, bottom). Consistent with V_(H)1-46 antibodies, the mutated positions among V_(H)1-2 derived bnAbs also showed high frequency of mutation among non-HIV-1 targeting V_(H)1-2 antibodies, suggesting that gene mutability contributes to V_(H)1-2 derived HIV-1 antibody evolution. Notably, the average mutability of the V_(H)1-2 gene at positions where the CH235 antibody showed SHM was generally high: 9 of 15 positions mutated in CH235 antibody were also mutated in more than 15% of V_(H)1-2-derived NGS reads. In 10 of these 15 positions, the mature V_(H)1-2-derived bnAbs (VRC01, VRC-CH31 and VRC-PG04) also showed changes. When we analyzed mutability of other V_(H) genes used by CD4bs bnAbs (V_(H)1-69, V_(H)3-23, V_(H)3-30, and V_(H)4-59) (Zhou et al., 2015) (FIG. 50D), we observed gene mutability patterns different from that of V_(H)1-46 while, in contrast, the mutability patterns of V_(H)1-2 and V_(H)1-46 were more similar (FIG. 56C). Despite the similarity between V_(H)1-2 and V_(H)1-46, we did observe that antibody sequences from CD4bs bnAbs of each gene segregated phylogenetically (FIG. 50E), indicating differences in maturation pathway between bnAbs evolving from these two germline genes.

These data suggested that for both V_(H)1-2 and V_(H)1-46 germline genes-derived bnAbs, somatic mutations that lead to neutralization breadth appeared to be primarily determined by the intrinsic mutability of V_(H)1-46 and V_(H)1-2 germline genes. The differences in the intrinsic mutabilities of these V_(H) genes may contribute to the high occurrence of CD4bs bnAbs that originate from either V_(H)1-2 or V_(H)1-46 (Zhou et al., 2015).

Interaction Between CH235 and CH103 bnAb Lineages.

While gene mutability plays a role in determining the position where SHM occurs, binding between antibody and HIV-1 Env likely also plays a role in selecting or fixing a mutation. A hallmark of cooperating B cell lineages is that they interact at the same site as the bnAb lineage that is being driven (Gao et al., 2014).

To determine a mechanism whereby the initial interaction of the early CH235 and CH103 lineage members bind to the same or similar epitope and result in CH235 selection of escape mutants that stimulated the CH103 bnAb lineage (Gao et al., 2014), we evaluated cross-competition between early CH235 lineage antibodies and the CH103 lineage antibody CH106 in ELISA, as an example of early CH103 lineage development, and measured their association rate constant with surface plasmon resonance (SPR). Since both the CH235 and CH103 lineages bound to the loop D gp120 region, we asked if the early CH235 lineage antibodies could block the binding of the CH103 lineage mature antibody CH106, or block the binding of soluble (s)CD4 to CH505 TF gp120 Env. CH241 was the only antibody in the CH235 lineage that strongly blocked CH106 bnAb and sCD4 binding to CH505 gp120 (IC₅₀=2.6 and 1.5 μg/ml, respectively) (FIG. 57A).

To confirm early dominance of the binding of CH103 lineage compared to the CH235 lineage to CH505 TF Env, we reversed the blocking assay and asked if bnAb CH106 could block the binding of biotinylated CH235, CH236, CH239, CH240 or CH241. CH106 strongly blocked the binding of all the CH235 mature antibodies with IC50s ranging from 2.3 μg/ml (for CH240) to 14.3 μg/ml (for CH241) (FIG. 57B). These data suggested that the earliest maturation intermediates of the CH235 lineage antibodies could not outcompete CH106 bnAb for binding to CH505 TF gp120 Env.

Affinity maturation in germinal centers is subjected to kinetic selection and involves improvement in dissociation rate constant (K_(d)) that is often driven by an improvement in the kinetic association rate (k_(a)), which is a key variable in conferring a binding advantage for the cognate epitope to an antibody over other competing antibodies (Foote and Milstein, 1991; Kepler et al., 2014). We measured the k_(a) and dissociation kinetic rate (k_(d)) of the CH505 TF gp120 Env binding by CH235 and CH103 with SPR to identify differences that might explain the relative inability of the CH235 lineage to block the binding of the CH103 lineage bnAbs to autologous CH505 TF Env and found that the two lineages followed two distinct trajectories and modalities to increase their overall affinity.

The UCA of the CH103 lineage bound to CH505 TF Env with a K_(d) of 227 nM which increased one order of magnitude throughout affinity maturation (FIG. 44A). The CH103 UCA displayed a fast association rate (k_(a)=37×10³ M⁻¹s⁻¹) which was maintained across the intermediate and mature mAbs (k_(a)=11.9-37.3×10³ M⁻¹s⁻¹), suggesting that maintaining the fast association rate was important for survival and maturation of the CH103 lineage (FIG. 44B). In contrast, the CH235 lineage mAb K_(d) increased four orders of magnitude during affinity maturation (from 30.6 mM of IA4—the earliest intermediate mAb in the CH235 lineage for which kinetic rates could be measured—to 0.7 nM of CH241) (FIG. 44C). Such increase was predominantly facilitated by slower dissociation rates (k_(d)) observed in later intermediates and mature mAbs, which decreased from 88.1×10⁻³ s⁻¹ of IA4 to 0.33×10⁻³ s⁻¹ of CH241 (FIG. 44D). Conversely, CH235 lineage mAbs bound to CH505 TF gp120 Env with k_(a) that started off an order of magnitude slower than CH103 UCA and its earlier intermediates (IA4 k_(a)=2.9×10³ M⁻¹s⁻¹) and only modestly improved—primarily between IA1 and CH235 mAbs—with the majority of the early CH235 mAbs having slower k_(a) than CH103 mAbs (FIG. 44D).

Thus, the relative inability of wk 41 CH235 lineage antibodies to block early mature CH103 lineage mAbs could be explained by the observed differences in their association rates, and these data provide an explanation of how the CH235 antibody lineage exerted its cooperating function in driving autologous virus toward better neutralization by the CH103 antibody lineage without impeding concurrent development of the CH103 antibody lineage itself.

Late CH235 Lineage Broadly Neutralizing Antibodies Neutralize Autologous Loop D Escape Viruses Selected by Early CH235 Lineage Members.

We have previously demonstrated that the CH235 lineage selected escape viruses with mutations in the loop D region of gp120 Env that rendered loop D mutant viruses more sensitive to the CH103 bnAb lineage and that autologous virus escaped from early CH235 lineage antibodies by wk 30 after infection (Gao et al., 2014). We have now isolated autologous viruses through wk 323 and determined the neutralization capacity of the late CH235 lineage bnAbs. Viruses partially sensitive to the later members of the CH235 lineage (particularly bnAbs CH235.9 and CH235.12) were found as late as wk 176 (FIG. 45A, FIG. 58). These viruses still contained the loop D mutations that were selected by virus escape from early antibody members of the CH235 lineage (Gao et al., 2014). Hence, we tested the ability of the late CH235 lineage bnAbs to neutralize the panel of CH505 TF loop D mutants (Gao et al., 2014). Remarkably, CH235.9, CH235.12 and CH235.13 bnAbs acquired the ability to neutralize all loop D mutants that were resistant to the early members of the CH235 lineage (FIG. 45B and FIG. 59). In particular, CH235.9, CH235.12 and CH235.13 neutralized CH505 TF gp120 M8, M20 and M21 (not neutralized by early lineage member CH236), which differed from CH505 TF gp120 M6 and M10 (neutralized by CH236) by a single mutation at position 280 (N280S for M8 and M20, and N280T for M21) (FIG. 45B).

In the gp120-complexed structure, the side chains of N280 forms three hydrogen bonds with two residues in the CDR L3 and these hydrogen bonds are predicted to be disrupted by the N280S and N280T mutations (FIG. 51A). Since the CH235.9 antibody had the V_(L) of CH236, the direct implication was that mutations in the heavy chain were responsible for the ability of CH235.9 to neutralize loop D mutant viruses. Interestingly, CH235.7, which did not neutralize autologous viruses beyond wk 53, also had the V_(L) of CH236 but, in contrast to CH235.9, failed to neutralize CH236-resistant loop D mutants M7, M8, M9, M20 and M21.

Therefore, we reverted the 5 amino acids (aa) in CH235.9 V_(H) at gp120 contact positions that were different from those present in CH236 V_(H) but not shared with CH235.7 V_(H): N30T and D31T in CDR H1, G62Q and G65Q in FR H3 and A103E in CDR H3 (FIG. 51B). Five of the six CH235.9 mutants retained the ability to potently neutralize all the CH505 TF loop D mutant viruses. In contrast, the N30T mutation in CDR H1 reverted CH235.9 to the CH236 phenotype (CH236 has a threonine in position 30): M21 neutralization was abrogated, M20, M7 and M9 were near completely abrogated (CH235.9 N30T IC₅₀>44 μg/ml) and M8 IC₅₀ increased 37-fold (CH235.9 IC₅₀=0.66 μg/ml vs CH235.9 N30T IC₅₀=24.31 μg/ml) (FIG. 59).

Thus, acquisition of extraordinary breadth in the CH235 bnAb lineage was associated with accumulation of somatic mutations in CDR H1 that enabled late CH235 lineage antibodies to neutralize autologous loop D mutant viruses that were escape mutants from early CH235 antibodies. CH235.9 bnAb residue N30 contacts R429 in the P20-P21 loop of the C4 region of gp120 Env, which is on the opposite face of the CD4bs from loop D (FIG. 45C). In addition, CH505 TF has a glutamic acid in position 429 that is in close enough proximity to N30 to form a hydrogen bond.

These findings indicate a mechanism for acquiring the ability to neutralize loop D mutants via a compensatory mutation in the CH235 V_(H)DJ_(H) which strengthens the binding to the gp120 C4 region by introducing hydrogen bonds that correct the loss of neutralization due to disruption of the hydrogen bonds between loop D and the CH235 mAb light chain.

CH235 and CH103 Lineage Antibody Binding to CH505 gp120 Env.

We tested the CH235 lineage antibodies for binding to 113 recombinant CH505 gp120 Env isolated from time of transmission to wk 160 post-transmission, including CH505 TF loop D mutant Envs (FIG. 46A and FIG. 60). Of note, CH235.9 and CH235.12 bound to 4/22 and 8/22 Envs isolated from wk 136 and 160 post-transmission, respectively, including Envs from viruses that were also neutralized. We have previously reported Env binding to the initial members of the CH103 lineage (Hraber et al., 2015), and have now performed the same Env binding analysis of the CH103 lineage with 10 additional matured bnAb members of the CH103 lineage (FIG. 46A and FIG. 60). We have used these data to select CH505 gp120 Env quasi-species that bound to mature and precursor bnAbs of both lineages, defining a series of CH505 Env immunogens now optimized and predicted to induce both bnAb lineages (FIG. 52A).

We had previously reported that CH235 UCA weakly reacted with CH505 TF gp120 at ˜10 M as determined by SPR (Gao et al., 2014). Here we show stronger binding of the CH235 UCA to 8/113 autologous CH505 gp120 Envs measured in ELISA (FIG. 46A and FIG. 60). Moreover, in a panel of 15 heterologous Envs from multiple clades, CH235 UCA bound to 3/15 Envs and the introduction of only 3 mutations (W47L, G54W and S56R), which were selected based on the increase in surface area of interaction (G54W and S56R) or the reduction in clash score (W47L), increased this recognition (to 5/15 Envs), of which the dominant effect appeared to be reduction in clash (FIG. 46B and FIG. 52B).

Autoreactivity in the CH235 B Cell Lineage.

Development of auto- and polyreactivity during antibody maturation toward neutralization breadth is a critical aspect that may limit the ability of generating bnAbs during natural infection and upon vaccination (Bonsignori et al., 2014; Haynes et al., 2005; Haynes et al., 2012; Haynes and Verkoczy, 2014; Liu et al., 2015; Verkoczy et al., 2013; Verkoczy et al., 2010; Verkoczy et al., 2011). We had previously reported that in HIV-1-infected individual CH505, the CD4bs CH103 bnAb lineage was polyreactive and, similar to VRC01-class bnAbs, bound to human ubiquitin ligase E3A (UBE3A) with avidity correlated with neutralization (Liao et al., 2013; Liu et al., 2015). In addition, most of the mutations introduced in VRC07—a somatic variant of VRC01—that enhanced neutralizing activity also resulted in increased autoreactivity (Rudicell et al., 2014). Since CH235.12 is a potent and extremely broad CD4-mimic CD4bs bnAb, we compared the auto- and polyreactivity profile of CH235.12 with other members of the CH235 lineage. Most CH235 lineage antibodies displayed reactivity against DNA and sporadic reactivity with Scl70 (CH235.7) (FIG. 47A). CH241 bound to cardiolipin (FIG. 47B). In Hep-2 IF staining CH236, CH235.7 and CH235.9 were all cytoplasmic positive (FIG. 47C). Conversely, CH235.12, despite being highly mutated and broadly neutralizing, did not display autoreactivity in any of these assays (FIG. 47A-C) Of particular note, CH235 lineage antibodies, including CH235.12, did not react with UBE3A (FIG. 47D).

These data identify CH235.12 as an antibody that has developed neutralization breadth without being itself auto- and polyreactive, while less mutated precursor antibodies (CH235 is in the same clade of CH235.12) did develop autoreactivity. We conclude that in vivo decoupling of neutralization breadth of CD4 mimic CD4bs bnAbs from auto- and polyreactivity can occur, even for bnAb lineages that have developed autoreactivity during the course of their maturation and, therefore, inducing such bnAbs from such lineages through vaccination, though difficult, is an achievable goal.

Discussion

Here we have traced the ontogeny of the CH235 V_(H)1-46 8ANC131 class of CD4bs bnAbs from acute infection to chronic infection and defined both the structural and functional pathways of bnAb lineage induction. That the CH235 bnAb lineage that selected virus escape mutants that drove the CH103 CD4bs CDR H3-dependent bnAb lineage is itself an 8ANC131-class bnAb lineage and co-evolved with the CH103 bnAb is a remarkable demonstration of a bnAb-to virus-to bnAb interaction in the same HIV-1 infected individual. In addition, the similarity of V_(H)1-46 8ANC131-like and V_(H)1-2 VRC01 family CD4 supersite bnAbs demonstrates dramatic convergence of antibody structures to recognize the CD4 supersite. The CH235 lineage required over 20% SHM in heavy chain variable domain to achieve 90% breadth. Fortunately, a substantial portion of the V_(H)-gene SHM was guided by the intrinsic mutability of the V_(H)1-46 germline gene. Moreover, the CH235 lineage Ab that became broadly neutralizing acquired the ability to neutralize loop D mutants selected by early Ab lineage members (Gao et al., 2014) with a mechanism involving a compensatory mutation (T30N) in CDR H1, which allowed the formation of H-bonds with the HIV-1 gp120 C4 region, thus correcting the original loss of binding.

The driving forces of the CH235 lineage were the natural transmitted/founder and M5 Envs. In addition, despite near-complete autologous virus escape from CH235 lineage antibodies by wk 100, viruses arose later during the course of infection, which were sensitive to the more mature CH235 bnAb members and likely contributed to antigen drive. It is interesting to note that many of these late viruses were less sensitive to CH103 CDR H3 binder bnAbs prompting the hypothesis that the CH103 lineage may have the capacity for cooperation with the CH235 lineage after 5-6 years of co-development. Finally, the CH235.12 antibody that evolved late in CH235 development is an extraordinary broad and potent non-autoreactive antibody and is a candidate for preventive and therapeutic uses.

In summary, the acquisition of neutralization breadth in the CH235 VRC01-like V_(H)1-46 CD4 mimic bnAb occurred with the sequence of transmitted/founder and early mutant-initiated antigen drive, selection of Env loop D mutants that cooperated with the CH103 bnAb lineage to drive it to bnAb breadth, followed by acquisition of the ability of the CH235 lineage itself to neutralize autologous loop D mutants coincident with potent neutralization of a broad array of heterologous HIV-1 isolates. Mapping these events points to a strategy for the simultaneous induction of both CDR H3 and VRC01-class CD4bs bnAbs, whereby sequential immunizations with transmitted founder Env followed by loop D mutant Envs comprise a rational immunization strategy.

Experimental Procedures

Donor and sample information. Donor and sample information was previously reported (Liao et al., 2013) and is summarized in Supplemental Experimental Procedures. Memory B cell cultures were performed on PBMCs collected at 264 and 323 wks post-transmission. All work related to human subjects was in compliance with Institutional Review Board protocols approved by the Duke University Health System Institutional Review Board.

Preparation of libraries for 454 DNA pyrosequencing. 454 DNA pyrosequencing was performed on genomic DNA template isolated with Qiagen kits from PBMCs collected at 6, 7, 8, 9, 14, 20, 22, 30, 41, 53, 66, 92, 100, 144 and 152 wks post-transmission as described in (Boyd et al., 2009) and in Supplemental Experimental Procedures. Only unique V-heavy rearrangements were included in the analysis to generate the phylogeny; in the case of duplicated sequences, the earliest occurrence was included in the analysis.

Phylogenetic analysis. For clonal phylogenetics, the UCA was inferred using Cloanalyst (Kepler, 2013), which simultaneously estimates the UCA and the phylogenetic tree relating the observed sequences to each other and to the UCA. Internally, Cloanalyst uses dnaml from the PHYLIP suite of phylogenetic software (Felsenstein, 2005). The CH235 antibody lineage clonogram was displayed using the ete2 Python package.

Isolation of CH235 Lineage Antibodies from Donor CH505. Fluorescence-activated cell sorting of antigen-specific IgG⁺ B cells from PBMC and the amplification and cloning of immunoglobulin genes were performed as described in (Bonsignori et al., 2011). CH505.TF gp120 Env-positive memory B cells were cultured as described in Supplemental Experimental Procedures.

Neutralization assays. Neutralization of donor CH235 mAbs were measured using single-round-of-infection HIV-1 Env pseudoviruses and TZM-bl target cells as described in Supplemental Experimental Procedures.

Neutralization signature. Antibody neutralization signatures were computed and compared as described in Supplemental Experimental Procedures.

Monoclonal Antibody and Antigen-Binding Fragment (Fab) Production. Ig genes of mAbs were amplified from RNA and expression plasmids for heavy and kappa chains were constructed. Expression and purification of recombinant IgG mAbs and preparation of Fab fragments are described in Supplemental Experimental Procedures.

Crystallization, X-Ray Data Collection, Structure Determination, and Refinement of Donor CH235 Antibodies in Complex with HIV-1 gp120. Purification, crystallization of antibody-gp120 complexes, data collection, structure solution, refinement and analysis are described in Supplemental Experimental Procedures. Diffraction data were integrated and scaled with the HKL2000 suite (Otwinowski and Minor, 1997).

Electron microscopy data collection and processing. BG505 SOSIP.664 and B41 SOSIP.664 gp140 trimers and donor CH235-derived Fab complex negative-stain electron microscopy images, analysis and visualization are described in the Supplemental Experimental Procedures.

Focused maturation and conformity analysis. Focused maturation and mAb conformity analysis are described in the Supplemental Experimental Procedures.

Surface Plasmon Resonance Affinity and Kinetics Measurements. MAb binding to autologous CH505 gp140 was measured using a BIAcore 3000 or BIAcore T200 instrument (GE Healthcare) as described in (Alam et al., 2007; Alam et al., 2009; Liao et al., 2013) and in Supplemental Experimental Procedures.

Direct-Binding ELISA. Direct-binding ELISAs were performed as described in Supplemental Experimental Procedures.

MAb CH235.9 Amino Acid Reversion. Site-directed mutagenesis of the CH235.9 mAb genes was performed using the Quikchange lightning multi-site-directed mutagenesis kit (Agilent) following manufacturer's protocol. Primers are listed in Supplemental Experimental Procedures.

Structural Modeling. Loop D mutations were structurally modeled using PyMOL with sidechains placed in the most frequently observed rotamer that did not result in steric clashing with neighboring residues. Hydrogen bonds were calculated using HBPLUS software (McDonald and Thornton, 1994).

Recombinant HIV-1 Proteins. HIV-1 genes of autologous CH505 Env were determined from samples collected from 4 to 323 wks post-infection by single genome amplification (Keele et al., 2008) and produced as described in (Liao et al., 2013).

Protein Array. MAbs were screened for binding on protein microarrays (ProtoArray) (PAH0525101; Invitrogen) pre-coated with 9,400 human proteins in duplicate and screened following manufacturer's instructions and as described in (Liu et al., 2015; Yang et al., 2013).

HEp-2 cell staining. Indirect immunofluorescence binding of mAbs or plasma to HEp-2 cells (Zeuss Scientific) was performed as previously described (Bonsignori et al., 2014; Haynes et al., 2005).

Supplemental Experimental Procedures

Donor and Sample Information.

The CH505 donor, from which the CH103 and the CH235 antibody lineages were isolated, is an African male enrolled in the CHAVI001 acute HIV-1 infection cohort (Tomaras et al., 2008) and followed for over 6 years. During this time viral load ranged from 14,460 to 847,279 copies/ml (median=173,667 copies/ml), and CD4 counts ranged from 69 to 431 cells/mm³ (median=294 cells/mm³).

The time of infection was estimated by analyzing the sequence diversity in the first available sample using the Poisson Fitter tool (Giorgi et al., 2010) as described in (Liao et al., Nature 2013). Results were consistent with a single founder virus establishing the infection and with the earliest isolated virus sequences being taken 4 weeks post-transmission.

Flow Cytometry, Memory B Cell Cultures and mAb Isolation.

The HIV-1 CH505.TF gp120 envelope glycoprotein was produced and used in flow cytometry on PBMC collected from donor CH505 at week 264 and 323 post-transmission using a two-color technique as described (Gray et al., 2011).

CH505.TF gp120Env-positive memory B cells were cultured as described (Bonsignori et al., 2011) with the following modifications: non-irradiated MS40L cells were used as feeder cells at a concentration of 3,000 cells/well and were added to wells in which memory B cells were sorted in bulk; 50 ng/ml of recombinant human (rHu) IL-21 (200-21; Peprotech, Rocky Hill, N.J.) were added to the complete medium; memory B cells were distributed by limiting dilution at a calculated concentration of 2 cells/well; culture medium was refreshed every 5 days.

Cell culture supernatants were screened for neutralization of autologous CH505.TF virus using the tzm-bl neutralization assay (Bonsignori et al., 2011; Montefiori, 2005) and for binding to CH505.TF gp120 Env, CH505.TF Δ371I gp120 Env mutant, HIV-1 Env resurface core protein 3 (RSC3) and RSC3 Δ371I (Wu et al., 2010).

MAbs CH235.10 through CH235.13 were isolated from cultures that displayed differential binding of CH505.TF and CH505 TF Δ371I gp120 Env, did not bind to RSC3 (Gao et al., 2014) and neutralized 13 to 99% CH505.TF infectivity.

CH235 lineage antibody frequency over total memory B cells was calculated by dividing the number of CH235 lineage antibodies isolated at week 41 (n=5; Gao et al., 2014) for the number of memory B cells analyzed (n=27,950). CH235 lineage antibody frequency over CH505.TF gp120 Env-specific memory B cells was calculated by dividing the number of CH235 lineage antibodies isolated at weeks 264 and 323 (n=4) for the number of CH505.Env gp120-specific memory B cells analyzed (n=794).

454 Pyrosequencing of CH235 Lineage Heavy Chains.

Antibody heavy chain gene rearrangements were PCR amplified from 6 independent 100 ng genomic DNA aliquots to generate 6 barcoded libraries per sample. Multiplexed primers complementary to the IGHV FR1 or FR2 framework regions, and an IGHJ-primer were modified from the BIOMED-2 consortium primers (Boyd et al., 2009; van Dongen et al., 2003). 10-nucleotide ‘barcode’ sequences in the primer sets encoded sample identity and replicate library identity. AmpliTaq Gold (Roche) enzyme was used for PCR following the manufacturer's instructions, with a thermocycler program: 94° C. 5 min; 35 cycles of (94° C. 30 sec, 60° C. 45 sec, 72° C. 90 sec); and final extension at 72° C. for 10 min. Following quantitation, PCR products from each replicate library were pooled in equimolar amounts, then the pooled library was run on a 1.5% agarose gel and gel extracted (Qiagen). High-throughput sequencing was performed on the 454 (Roche) platform using Titanium chemistry.

Antibody Production.

Immunoglobulin genes of mAbs CH235.10 through CH235.13 were amplified from RNA from isolated cells, expression cassettes made, and mAbs expressed as described (Gao et al. 2014). The V_(H) genes of mAbs CH235.6 through CH235.9 were retrieved from sequences obtained through genomic DNA 454 sequencing, which were restored to full length and complemented with the V_(L) of the phylogenetically closest isolated antibody in the CH235 lineage (i.e. CH241 for CH235.6 and CH235.8, and CH236 for CH235.7 and CH235.9). We have previously described the isolation of mAbs CH235, CH236, CH239, CH240 and CH241 and the inference of unmutated common ancestor (UCA) and intermediate antibodies IA1 through IA4 (Gao et al., 2014; Kepler, 2013).

Heavy chain plasmids were co-transfected with appropriate light chain plasmids at an equal ratio in Expi 293 cells using either 293Fectin or ExpiFectamine 293 transfection reagents (Thermo Fisher Scientific) according to the manufacturer's protocols. Cultures were supplemented with AbBooster antibody expression enhancer media (ABI Scientific) at 10% of the final culture volume 24 h after transfection. Cultures were then incubated at 33° C. for 5 more days, and supernatants were harvested and passed over a protein A affinity column. Following PBS wash and low pH elution, the pH of eluate was neutralized with 1MTris pH 8.5 and samples were dialyzed against PBS. Antibodies were then aliquoted and stored at −80° C. prior to use. Alternatively, for ExpiFectamine transfections we used the enhancer provided with the kit, transfected cultures were incubated at 37° C. 8% CO₂ for 2-6 days, harvested, concentrated and incubated overnight with Protein A beads at 4° C. on a rotating shaker before loading the bead mixture in columns for purification; following PBS/NaCl wash, eluate was neutralized with trizma hydrochloride and antibody concentration was determined by Nanodrop. Purified antibodies were tested in SDS-Page Coomassie and western blots, and stored at 4° C.

Direct-Binding ELISA.

Direct-binding ELISAs were performed as described previously (Bonsignori et al., 2011) with the following modifications: plates were blocked for 1 h at room temperature (RT) or overnight at 4° C. (both procedures were previously validated); primary purified antibodies were tested at a starting concentrations of 100 μg/ml, serially three-fold diluted and incubated for 1 h at RT; HRP-conjugated human IgG antibody was added at optimized concentration of 1:30,000 in assay diluent for 1 hour and developed using TMB substrate; plates were read at 450 nm in a SpectraMax 384 PLUS reader (Molecular Devices, Sunnyvale, Calif.); results are reported as logarithm area under the curve (LogAUC) unless otherwise noted.

For cell culture supernatant screening of RSC3 and RSC3 Δ371I HIV-1 Env core proteins reactivity, plates were coated with streptavidin (2 μg/ml); blocked plates were stored at −20° C. until used; 10 μl/well of biotinylated avi-tagged RSC3 and RSC3 Δ371I were added at 2 μg/ml for 30 minutes at RT and culture supernatants were added at 1:3 dilution in assay diluent; plates were developed for 10 min using SureBlue Reserve TMB (53-00-03; KPL, Gaithersburg, Md.) equilibrated at RT.

Competition ELISAs were performed using 10 μl of primary purified monoclonal antibody, starting at 100 μg/ml and diluted in a two-fold concentration, incubated for 1 h at RT; for CD4 binding site blocking assays, 10 μl of a saturating concentration soluble CD4 (Progenics Pharm Inc.) was added following antibody incubation step. Ten μl of biotinylated target Mab was added at the EC50 determined by a direct binding of biotinylated-Mab for one hour at RT. After background subtractions, percent inhibition was calculated as follows: 100-(sera triplicate mean/no inhibition control mean)*100.

Autoimmune purified antigens histones (whole), Jo-1, RNP/Sm, Scl-70, Sm, SSA (Ro), SSB (all from ImmunoVision) and centromere B (Prospec) were coated at optimal concentrations determined by lot-specific checkerboard with positive controls. All plasma antibody positive controls were purchased from ImmunoVision; lot-specific optimal ranges for standard curves were determined. All antibodies were tested using the same lots for each antigen and positive controls with the protocol described above. For DNA ELISA, plates were coated with 2 μg/ml poly-lysine (Sigma-Aldrich) for 2 h at RT, washed 3× with PBS and blocked with PBS/2%/BSA/0.05% Tween-20 for 2 h at RT. After 3× wash, DNA (LS002195, Worthington) in saline sodium citrate buffer was added for 1 h, washed and antibodies were incubated for 1 h. Secondary antibody was diluted in PBS/0.05% Tween-20. Plates were developed for 30 min. Human recombinant monoclonal antibody Ab008391 (courteously provided by David Easterhoff, Duke Human Vaccine Institute) was used as positive control. For all autoantigen ELISAs, palivizumab was used as negative control. For each antibody, LogAUC was calculated and data are presented semi-quantitatively: no binding=logAUC_(Ab)≤2× negative control logAUC_(neg ctrl); to quantify antibody binding we divided (logAUC_(pos ctrl)−2× logAUC_(neg ctrl)) in tertiles and expressed test antibody binding as weak (+), intermediate (++) or strong (+++) if logAUC_(Ab) was in the first, second or higher tertile, respectively.

Anti-cardiolipin ELISA was performed using the QUANTA Lite ACA IgG III kit (708625; INOVA Diagnostics) following manufacturer's protocol.

Assessment of Virus Neutralization Using a Large Panel and Calculation of Neutralization Dendrograms.

Neutralizing antibody assays in TZM-bl cells were performed as described previously (Montefiori, 2005). Neutralization breadth of CH235 UCA, CH235, CH235.9 and CH235.12 neutralization breadth was assessed using the 384-well plate declination of the assay using an updated panel of 199 geographically and genetically diverse Env-pseudoviruses representing the major circulating genetic subtypes and recombinant forms as described (Seaman et al., 2010; Wu et al., 2010). The data were calculated as a reduction in luminescence units compared with control wells, and reported as IC₅₀ in μg/ml (Montefiori, 2005).

Dendrograms were calculated using the neighbor-joining method, showing the protein sequence distance from the HIV-1 Env gp160 sequences of 190 HIV-1 primary isolates. The clades of HIV-1, including circulating recombinant forms (CRFs) are indicated.

Antibody Neutralization Fingerprinting Analysis.

Neutralization fingerprints were computed and compared for CH235, CH235.9 and CH235.12 from the CH235 lineage, other CD4-binding-site antibodies, and antibodies targeting other sites of vulnerability on HIV-1 Env. The fingerprints were computed over a common panel of 165 HIV-1 strains with neutralization data for all antibodies, and a hierarchical clustering procedure was applied for building the tree, as described in (Georgiev et al., 2013). Briefly, for each antibody, the neutralization data for the common set of 165 HIV-1 strains formed that antibody's neutralization fingerprint. The Spearman correlation coefficients for all pairs of antibody neutralization fingerprints were then computed, transforming the antibody-virus neutralization matrix into an antibody-antibody correlation matrix. This correlation matrix was then input into a hierarchical clustering procedure as a way to visualize the similarities between the neutralization fingerprints for the different antibodies. The distances in the resulting tree are thus a function of the differences between fingerprints.

VH1-46 and VH1-2 Antibody Dendrogram Calculation.

Phylogenic trees for multiple antibodies derived from VH1-46 and VH1-2 heavy chain variable genes were calculated using the neighbor-joining method. The sequences are aligned by Clustal Omega, calculated using ClustalW2. Dendrograms were drawn in Figtree.

Production and Purification of HIV-1 Env Protein Complexed to Antigen-Binding Fragments.

HIV-1 gp120 protein from clade AE 93TH057 and antibodies of CH235, CH235.9 and CH235.12 were produced and purified as described previously (Zhou et al., 2010). Fab fragments of antibodies were prepared by digesting purified IgG with Lys-C at 37° C. for 2-4 h. The digestion reaction was quenched by the addition of cOmplete protase inhibitors (Roche). The digested antibodies were passed over Protein A agarose to remove the Fc fragment. The Fab was further purified over a Superdex 200 gel filtration column and concentrated aliquots were stored at −80° C.

X-Ray Crystallography.

The gp120-antibody complexes were formed by mixing deglycosylated gp120 with the antibody Fab in a 1:1.5 molar ratio. The complexes were purified by size exclusion chromatography (Hiload 26/60 Superdex S200 prep grade; GE Healthcare) with buffer containing 0.35 M NaCl, 2.5 mM Tris (pH 7.0), and 0.02% NaN₃. Fractions with gp120-antibody complexes were concentrated to ˜10 mg/ml and used for crystallization experiments. All gp120-Fab complexes were screened against 576 crystallization conditions using a Cartesian Honeybee crystallization robot. Initial crystals were grown by the vapor diffusion method in sitting drops at 20° C. by mixing 0.2 μl of protein complex with 0.2 μl of reservoir solution. Crystals were manually reproduced in hanging drops by mixing 0.50 μl protein complex solution with 0.5 μreservoir solution.

The 93TH057 core_(e) gp120-CH235 complex was crystallized with a reservoir solution of 25% (w/v) of PEG2000, 0.2 M of Li₂SO₄, 0.1 M of Tris-HCl pH 8.5 and 5% (v/v) of isopropanol and was flash frozen in liquid nitrogen in mother liquor supplemented with 15% of 2R,3R-butanediol as a cryoprotectant. The 93TH057 core_(e) gp120-CH235.9 complex was crystallized with a reservoir solution of 9% (w/v) of PEG8000, 19% (w/v) of PEG400, 0.1 M HEPES pH 7.5 and was flash frozen in mother liquor supplemented with an additional 15% PEG 400 as a cryoprotectant. The 93TH057 core_(e) gp120-CH235.12 complex was crystallized with a reservoir solution of 10% PEG 8000, 20% PEG 400 and 100 mM HEPES, pH7.5 and was flash frozen in mother liquor supplemented with an additional 15-20% PEG 400 as a cryoprotectant.

Data for all crystals were collected at a wavelength of 1.00 Å at SER-CAT beamlines ID-22 and BM-22 (Advanced Photon Source, Argonne National Laboratory). All diffraction data were processed with the HKL2000 suite, structures were solved by molecular replacement using PHASER, and iterative model building and refinement were performed in COOT and PHENIX, respectively. For 93TH057core_(e) complexes with CH235.9 and CH235.12, molecular replacement solutions were obtained using EAF31403.1-CH235 complex as a search model.

Throughout the refinement processes, a cross validation (R_(free)) test set consisting of 5% of the data was used and hydrogen atoms were included in the refinement model. Structure validations were performed periodically during the model building/refinement process with MolProbity. The 93TH057 core_(e)-CH235 structure was refined to a final R_(free) value of 22.9% with 96% residues in the favored region of the Ramachandran plot, and 0.1% outliers. The 93TH057 core_(e)-CH235.9 structure was refined to a final R_(free) value of 22% with 97.1% residues in the favored region of the Ramachandran plot, and 0% outliers. The 93TH057 core_(e)-CH235.12 structure was refined to a final R_(free) value of 23% with 97.0% residues in the favored region of the Ramachandran plot, and 0.1% outliers. All figures containing representations of the protein crystal structures were made with PyMOL. Gp120 and antibody interactions were analyzed with the PISA server.

Surface Plasmon Resonance Affinity and Kinetics Measurements.

For kinetic measurement, each antibody was captured on an anti-human IgFc immobilized sensor surface (200-500RU) and gp120 proteins at varying concentrations were injected to monitor association and dissociation phases. Buffer reference and non-specific binding to a control antibody (palivizumab) captured surface were used to derive specific binding signals. Kinetic rate constants and dissociation constant (Kd) were derived from global curve fitting analysis using a Langmuir 1:1 interaction model using the BIAevaluation 4.1 software (GE Healthcare).

Electron Microscopy Data Collection and Processing.

BG505 SOSIP.664 and B41 SOSIP.664 gp140 trimers were expressed in HEK293F cells and purified by 2G12-affinity and gel filtration chromatography as described elsewhere (Pugach et al., 2015; Sanders et al., 2013). Trimers were incubated with a 10 molar excess of Fab (CH235, CH235.9, or CH235.12) overnight at room temperature and the complexes were diluted to ˜0.03 mg/mL prior to application onto a carbon-coated 400 Cu mesh grid that had been glow discharged at 20 mA for 30 s. The grids were stained with 2% (w/v) uranyl formate for 60 seconds. Samples were imaged using a FEI Tecnai T12 electron microscope operating at 120 keV, with an electron dose of ˜25 e⁻/Å² and a magnification of 52,000× that resulted in a pixel size of 2.05 Å at the specimen plane. Images were acquired with Leginon (Suloway et al., 2005) using a Tietz TemCam-F416 CMOS camera with a nominal defocus range of 1000-1500 nm. Automated particle picking, stack creation, and initial 2D classification was performed in the Appion software suite (Lander et al., 2009). Noise and junk particles were discarded and the remaining stack was subjected to 3D classification using Relion (Scheres, 2012) with an EM volume created from the x-ray structure of ligand-free BG505 SOSIP.664 (PDB: 4zmj) low pass filtered to 60 Å as the reference model. While both CH235.9 and CH235.12 bound to either B41 or BG505 at predominantly full stoichiometry (3 Fabs per trimer), CH235 bound to either trimer at sub-stoichiometric ratios (1 Fab per BG505 trimer and 2 Fabs per B41 trimer). The 3D classes representing the predominant stoichiometry for each complex were used as the initial models (low pass filtered to 40 Å) for further refinement using Relion, with C3 symmetry imposed for complexes with CH235.9 or CH235.12. The total number of particles used in refinement and final resolution of the map using a Fourier shell correlation of 0.5 are as follows: BG505 in complex with CH235—3,467 particles (˜25 Å); B41 in complex with CH235—4,248 particles (˜24 Å); BG505 in complex with CH235.9-2,567 particles (25 Å); B41 in complex with CH235.9-8,061 particles (19 Å); BG505 in complex with CH235.12-15,565 particles (17 Å); B41 in complex with CH235.12-17,023 particles (16 Å).

To create figures of each Fab in complex with a representative trimer, the 3D reconstructions for each complex were fit into an EM volume created from the x-ray structure of unliganded BG505 SOSIP.664 (PDB: 4ZMJ) low pass filtered to 30 Ain UCSF Chimera (Pettersen et al., 2004) and using the “segment map” option to isolate the density of the Fab components alone. Two-dimensional back projections of the final 3D models were generated using EMAN (Tang et al., 2007).

Epitope Visualization.

The HIV-1 gp120 epitopes targeted by donor CH235 antibodies were visualized using PyMOL (Schrodinger, 2010). In this graphic program, we used 5.5-Å distance for selection of epitope atom sets which were virtually identical to those defined by protein interface analysis program PISA.

Monoclonal Antibody CH235.9 Amino Acid Reversion.

Primers were designed with the online Agilent Quikchange primer designer tool (www.thermofisher.com) and were as follows:

CH235.9_(N30T): (SEQ ID NO: 8) CGTGGCGTCTGGATACAACTTCACCGACTACTATATAC; CH235.9_(D31T): (SEQ ID NO: 9) CGTCTGGATACAACTTCAACACCTACTATATACACTGGGTGC; CH235.9_(G62Q): (SEQ ID NO: 10) GGTCGCACAGATTACGCACAGGCGTTTGGGGA; CH235.9_(G65Q): (SEQ ID NO: 11) GATTACGCAGGGGCGTTTCAGGACAGAGTGTCCA; CH235.9_(A103E): (SEQ ID NO: 12) GTTAGAAATGTGGGAACGGAGGGCAGCTTGCTCCACTATG; CH235.9_(G62Q/G65Q): (SEQ ID NO: 13) GGTCGCACAGATTACGCACAGGCGTTTCAGGACAGAGTGTCCA; CH235.9_(S54R): (SEQ ID NO: 14) GGATCGACCCTAGGGGTGGTCGCACAG; CH235.9_(A61S): (SEQ ID NO: 15) GTGGTCGCACAGATTACTCAGGGGCGTTTG.

Presence of mutations in plasmid products was confirmed by single-colony sequencing.

Structural Bioinformatics.

Average buried surface area (BSA) on gp120 was calculated for residues with BSA>1 Å² for the gp120-antibody complexes, and the corresponding antibody neutralization potencies were averaged for each of those residues based on data from neutralization assays. Spearman correlation between BSA on gp120 and antibody potencies was calculated for BSA cutoffs=0 to 85 Å² and potency logIC₅₀ cutoffs=0.60 to 1.62 μg/ml.

Sample Preparation for 5′ RACE Method and 454 Pyrosequencing.

Human PBMCs (6×10⁷) were obtained from three HIV-1 and hepatitis C negative individuals (LP32647, LP08248 and LP23810). A 5′RACE approach was developed to amplify immunoglobulin genes based on previously described methods (Venturi et al., 2011). Briefly, the PBMCs were pelleted at 1200 rpm for 8 min. mRNA was then extracted and eluted in 50 μl elution buffer using MACS mRNA isolation kit (Miltenyi Biotec) according to manufacturer's instructions. To synthesize cDNA, 10 μl mRNA was mixed with 1 μl 5′CDS Oligo dT primers (12 μM) and incubated at 70° C. for 1 min and then −20° C. for 1 min. Then 1 μl SMARTER Oligo Primer (12 μM) (Clontech), 4 μl 5× RT buffer, 1 μl DTT 20 (20 mM), 1 μl dNTP (10 mM), 1 μl RNAse out and 1 μl SuperScript II reverse transcriptase (Invitrogen) were added to the reaction. After 2 hours incubation at 42° C., the cDNA products were purified using Nucleospin II kit (Macherey-Nagel) and eluted in 50 μl water. 454 pyrosequencing was performed as described previously (Wu et al., 2011). The first PCR amplification was performed with a common 5′ primer II A (Clontech) and an Ig gene specific 3′ primer (5′GGGGAAGACCGATGGGCCCTTGGTGG3′ (SEQ ID NO: 16)) using KAPA HIFI qPCR kit (Kapa Biosystems). The PCR products were purified with 2% Size Select Clonewell E-gel (Invitrogen) and Agencourt AMPure XP beads (Beckman Coulter). The second PCR amplification was performed with primers with 454 sequencing adapters (454-RACE-F: 5′CCATCTCATCCCTGCGTGTCTCCGACTCAGAAGCAGTGGTATCAACGCAGAGT3′ (SEQ ID NO: 17); 454-IgG-R: 5′CCTATCCCCTGTGTGCCTTGGCAGTCTCAGGGGGAAGACCGATGGGCCCTTGGT GG3′ (SEQ ID NO: 18)). The PCR products were again purified with 2% Size Select Clonewell E-gel and Agencourt AMPure XP beads.

Germline V Gene Specific Substitution Profile.

The raw reads from three healthy donors shorter than 300 nucleotides or longer than 600 nucleotides in length were not analyzed. Germline V gene was then assigned to each read using an in-house bioinformatics pipeline (Wu et al., 2015). We removed reads containing stop codons. Functional reads were then clustered using Usearch at 97% sequence identity, and one unique sequence was selected from each cluster to derive a curated dataset. To further reduce reads containing sequencing errors in the curated dataset, unique sequences having only one read in the clustering step were excluded. Finally, the curated dataset of the three donors were pooled for substitution frequency analyses.

Reads from the curated dataset that were assigned to germline V genes of interest were extracted, and were aligned using MUSCLE (Edgar, 2004). The amino acid substitution frequency or mutability of a V gene position was calculated by counting how many reads contain amino acids that are different from the germline V gene, and normalized by the total number of reads. We further calculated the frequency of the 19 types of amino acid substitutions at a position, which was used to generate positional substitution logo. The similarity of positional substitution frequency profiles between V genes of interest was measured by Pearson correlation coefficient.

Conformity Analysis.

The positional conformity of a conforming antibody sequence A to a reference sequence B is defined as the number of mutated positions shared by both sequences divided by the total number of mutations in the conforming sequence. Thus:

${c_{p}\left( {A;B} \right)} = \frac{{M_{A}\bigcap M_{B}}}{M_{A}}$

where M_(i) represents the set of amino acid positions in sequence i which are mutated from the germline V residue. Insertions and missing data are ignored, but deletions relative to the germline V are counted as mutations. For 8ANC131 and CH235 (Figure S3A):

M_(8ANC131)={2, 9, 10, 11, 16, 19, 20, 23, 26, 30, 31, 32, 33, 34, 37, 45, 46, 48, 50, 52, 53, 55, 57, 58, 59,60,62,63,66,68,69,70,71,74,77, 80, 84, 85, 88, 89}

M_(CH235)={19, 23, 31, 34, 46, 47, 50, 52, 55, 57, 59, 63, 68, 83, 84}

M_(8ANC131)∩M_(CH235)={19, 23, 31, 34, 46, 50, 52, 55, 57, 59, 63, 68, 84}

c_(p)(8ANC131, CH235)=13/15=86.7%

Identity conformity was defined the number of positionally conforming sites in conforming antibody A which were also mutated to the same residue as in the reference antibody B. Thus:

${c_{i}\left( {A;B} \right)} = \frac{\sum_{x \in {\{{M_{A}\bigcap M_{B}}\}}}\delta_{A_{x}B_{x}}}{M_{A}}$ where δ is the Kronecker delta function and A_(x) is the identity of the residue at position x of sequence A. For 8ANC131 and CH235 (Figure S3B): c_(i)(8ANC131, CH235)=4/15=26.7%

Targeting Precision of CD4bs-Directed Antibodies.

The targeting precision of the CD4bs-directed antibodies was defined as the buried surface area inside of the CD4 binding site minus the buried surface area outside of the CD4 binding site. The buried surface area of each antigen residue was determined by NACCESS. The buried surface area from the following residue numbers were considered inside of the CD4 binding site: 257, 279, 280, 281, 282, 283, 365, 366, 367, 368, 370, 371, 455, 456, 457, 458, 459, 460, 469, 472, 473, 474, 475, 476, and 477 (Zhou et al., 2007). The buried surface areas from the rest of the residues were considered outside of the CD4 binding site. Somatic hypermutation was defined using nucleotide sequences and P values were calculated based on linear regression.

Antibody Binding Orientation Calculation.

To calculate the relative rotation angles and translation to gp120-bound CD4 for gp120-bound CD4-binding site antibodies, all antibody-gp120 complexes to be analyzed were first superposed over the outer domain of gp120 (residue ranges: 252-392, 412-422, 437-476) with gp120 in its CD4 complex (PDB ID: 2NXY). The calculations of rotation angles and translation were then carried out with the gp120-aligned structures. For comparison of position of heavy chain variable domain relative to gp120-bound CD4, the frame work regions (residues 46-52, 56-59, 66-71 and 76-82) were superimposed to regions of CD4 domain 1 (residues 34-40, 43-46, 54-59, 65-71). The superposition procedures were performed with the Superpose Molecules module in CCP4 (Collaborative Computational Project, 1994). The Chi angle and distance between centroids in the Superpose output was taken as the rotation angle and translation distance between CD4 and a CD4-binding site antibody.

Supplemental References

-   Collaborative Computational Project (1994). The CCP4 suite: programs     for protein crystallography. Acta Crystallogr., Sect D: Biol.     Crystallogr. 50, 760-763. -   Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high     accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. -   Giorgi, E. E., Funkhouser, B., Athreya, G., Perelson, A. S.,     Korber, B. T., Bhattacharya, T. (2010). Estimating time since     infection in early homogeneous HIV-1 samples using a poisson model.     BMC Bioinformatics 11, 532. -   Gray, E. S., Moody, M. A., Wibmer, C. K., Chen, X., Marshall, D.,     Amos, J., Moore, P. L., Foulger, A., Yu, J. S., Lambson, B., et al.     (2011). Isolation of a monoclonal antibody that targets the alpha-2     helix of gp120 and represents the initial autologous     neutralizing-antibody response in an HIV-1 subtype C-infected     individual. J. Virol. 85, 7719-7729. -   Lander, G. C., Stagg, S. M., Voss, N. R., Cheng, A., Fellmann, D.,     Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P. W., et     al. (2009). Appion: an integrated, database-driven pipeline to     facilitate EM image processing. J. Struct. Biol. 166, 95-102. -   Montefiori, D. C. (2005). Evaluating neutralizing antibodies against     HIV, SIV, and SHIV in luciferase reporter gene assays. Current     protocols in immunology/edited by John E Coligan [et al] Chapter 12,     Unit 12 11. -   Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S.,     Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004). UCSF     Chimera—a visualization system for exploratory research and     analysis. J. Comput. Chem. 25, 1605-1612. -   Scheres, S. H. (2012). A Bayesian view on cryo-EM structure     determination. J. Mol. Biol. 415, 406-418. -   Seaman, M. S., Janes, H., Hawkins, N., Grandpre, L. E., Devoy, C.,     Giri, A., Coffey, R. T., Harris, L., Wood, B., Daniels, M. G., et     al. (2010). Tiered categorization of a diverse panel of HIV-1 Env     pseudoviruses for assessment of neutralizing antibodies. J. Virol.     84, 1439-1452. -   Schrodinger, LLC (2010). The PyMOL Molecular Graphics System,     Version 1.3r1. -   Suloway, C., Pulokas, J., Fellmann, D., Cheng, A., Guerra, F.,     Quispe, J., Stagg, S., Potter, C. S., and Carragher, B. (2005).     Automated molecular microscopy: the new Leginon system. J. Struct.     Biol. 151, 41-60. -   Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees,     I., and Ludtke, S. J. (2007). EMAN2: an extensible image processing     suite for electron microscopy. J. Struct. Biol. 157, 38-46. -   Tomaras, G, D, Yates, N. L., Liu, P., Qin, L., Fouda, G. G.,     Chavez, L. L., Decamp, A. C., Parks, R. J., Ashley, V. C., Lucas, J.     T., et al. (2008). Initial B-cell responses to transmitted human     immunodeficiency virus type 1: virion-binding immunoglobulin M (IgM)     and IgG antibodies followed by plasma anti-gp41 antibodies with     ineffective control of initial viremia. J. Virol. 82, 12449-12463 -   van Dongen, J. J., Langerak, A. W., Bruggemann, M., Evans, P. A.,     Hummel, M., Lavender, F. L., Delabesse, E., Davi, F., Schuuring, E.,     Garcia-Sanz, R., et al. (2003). Design and standardization of PCR     primers and protocols for detection of clonal immunoglobulin and     T-cell receptor gene recombinations in suspect lymphoproliferations:     report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 17,     2257-2317. -   Venturi, V., Quigley, M. F., Greenaway, H. Y., Ng, P. C., Ende, Z.     S., McIntosh, T., Asher, T. E., Almeida, J. R., Levy, S., Price, D.     A., et al. (2011). A mechanism for TCR sharing between T cell     subsets and individuals revealed by pyrosequencing. J Immunol. 186,     4285-4294. -   Wu, X., Yang, Z. Y., Li, Y., Hogerkorp, C. M., Schief, W. R.,     Seaman, M. S., Zhou, T., Schmidt, S. D., Wu, L., Xu, L., et al.     (2010). Rational design of envelope identifies broadly neutralizing     human monoclonal antibodies to HIV-1. Science 329, 856-861. -   Wu, X., Zhang, Z., Schramm, C. A., Joyce, M. G., Kwon, Y. D., Zhou,     T., Sheng, Z., Zhang, B., O'Dell, S., McKee, K., et al. (2015).     Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years     of Chronic HIV-1 Infection. Cell 161, 470-485. -   Zhou, T., Xu, L., Dey, B., Hessell, A. J., Van Ryk, D., Xiang, S.     H., Yang, X., Zhang, M. Y., Zwick, M. B., Arthos, J., et al. (2007).     Structural definition of a conserved neutralization epitope on HIV-1     gp120. Nature 445, 732-737.

Accession Numbers

Coordinates and structure factors for CH235, CH235.9 and CH235.12 in complex with HIV-1 gp120 have been deposited with the Protein Data Bank (PDB ID 5F9W, 5F90 and 5F96). Next-generation sequencing data have been deposited with the NCBI Sequence Reads Archive (SRP067168). Antibody heavy and light chains have been deposited with GenBank (KU570032-KU570053).

Antibodies Names correlation: See supra.

References for Example 8

-   Alam, S. M., McAdams, M., Boren, D., Rak, M., Scearce, R. M., Gao,     F., Camacho, Z. T., Gewirth, D., Kelsoe, G., Chen, P., et al.     (2007). The role of antibody polyspecificity and lipid reactivity in     binding of broadly neutralizing anti-HIV-1 envelope human monoclonal     antibodies 2F5 and 4E10 to glycoprotein 41 membrane proximal     envelope epitopes. J. Immunol. 178, 4424-4435. -   Alam, S. M., Morelli, M., Dennison, S. M., Liao, H. X., Zhang, R.,     Xia, S. M., Rits-Volloch, S., Sun, L., Harrison, S. C., Haynes, B.     F., et al. (2009). Role of HIV membrane in neutralization by two     broadly neutralizing antibodies. Proc. Natl. Acad. Sci. U.S.A. 106,     20234-20239. -   Bonsignori, M., Alam, S. M., Liao, H. X., Verkoczy, L., Tomaras, G.     D., Haynes, B. F., and Moody, M. A. (2012). HIV-1 antibodies from     infection and vaccination: insights for guiding vaccine design.     Trends Microbiol. 20, 532-539. -   Bonsignori, M., Hwang, K. K., Chen, X., Tsao, C. Y., Morris, L.,     Gray, E., Marshall, D. J., Crump, J. A., Kapiga, S. H., Sam, N. E.,     et al. (2011). Analysis of a clonal lineage of HIV-1 envelope V2/V3     conformational epitope-specific broadly neutralizing antibodies and     their inferred unmutated common ancestors. J. Virol. 85, 9998-10009. -   Bonsignori, M., Wiehe, K., Grimm, S. K., Lynch, R., Yang, G.,     Kozink, D. M., Perrin, F., Cooper, A. J., Hwang, K. K., Chen, X., et     al. (2014). An autoreactive antibody from an SLE/HIV-1 individual     broadly neutralizes HIV-1. J. Clin. Invest. 124, 1835-1843. -   Boyd, S. D., Marshall, E. L., Merker, J. D., Maniar, J. M.,     Zhang, L. N., Sahaf, B., Jones, C. D., Simen, B. B., Hanczaruk, B.,     Nguyen, K. D., et al. (2009). Measurement and Clinical Monitoring of     Human Lymphocyte Clonality by Massively Parallel V-D-J     Pyrosequencing. Sci. Transl. Med. 1. -   Dosenovic, P., von Boehmer, L., Escolano, A., Jardine, J.,     Freund, N. T., Gitlin, A. D., McGuire, A. T., Kulp, D. W., Oliveira,     T., Scharf, L., et al. (2015). Immunization for HIV-1 Broadly     Neutralizing Antibodies in Human Ig Knockin Mice. Cell 161,     1505-1515. -   Felsenstein, J. (2005). PHYLIP (Phylogeny Inference Package), 3.6a3     edn (Seattle, Wash.: distributed by the author: Department of Genome     Sciences, University of Washington). -   Foote, J., and Milstein, C. (1991). Kinetic maturation of an immune     response. Nature 352, 530-532. -   Gao, F., Bonsignori, M., Liao, H. X., Kumar, A., Xia, S. M., Lu, X.,     Cai, F., Hwang, K. K., Song, H., Zhou, T., et al. (2014).     Cooperation of B cell lineages in induction of HIV-1-broadly     neutralizing antibodies. Cell 158, 481-491. -   Georgiev, I. S., Doria-Rose, N. A., Zhou, T. Q., Do Kwon, Y.,     Staupe, R. P., Moquin, S., Chuang, G. Y., Louder, M. K., Schmidt, S.     D., Altae-Tran, H. R., et al. (2013). Delineating Antibody     Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate     Neutralization. Science 340, 751-756. -   Haynes, B. F. (2015). New approaches to HIV vaccine development.     Curr. Opin. Immunol. 35, 39-47. -   Haynes, B. F., and Bradley, T. (2015). Broadly Neutralizing     Antibodies and the Development of Vaccines. JAMA 313, 2419-2420. -   Haynes, B. F., Fleming, J., St Clair, E. W., Katinger, H., Stiegler,     G., Kunert, R., Robinson, J., Scearce, R. M., Plonk, K., Staats, H.     F., et al. (2005). Cardiolipin polyspecific autoreactivity in two     broadly neutralizing HIV-1 antibodies. Science 308, 1906-1908. -   Haynes, B. F., Kelsoe, G., Harrison, S. C., and Kepler, T. B.     (2012). B-cell-lineage immunogen design in vaccine development with     HIV-1 as a case study. Nat. Biotechnol. 30, 423-433. -   Haynes, B. F., and Verkoczy, L. (2014). AIDS/HIV. Host controls of     HIV neutralizing antibodies. Science 344, 588-589. -   Hraber, P., Korber, B., Wagh, K., Giorgi, E. E., Bhattacharya, T.,     Gnanakaran, S., Lapedes, A. S., Learn, G. H., Kreider, E. F., Li,     Y., et al. (2015). Longitudinal Antigenic Sequences and Sites from     Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV     Variants. Viruses 7, 5443-5475. -   Hraber, P., Seaman, M. S., Bailer, R. T., Mascola, J. R.,     Montefiori, D. C., and Korber, B. T. (2014). Prevalence of broadly     neutralizing antibody responses during chronic HIV-1 infection. AIDS     28, 163-169. -   Jardine, J., Julien, J. P., Menis, S., Ota, T., Kalyuzhniy, O.,     McGuire, A., Sok, D., Huang, P. S., MacPherson, S., Jones, M., et     al. (2013). Rational HIV immunogen design to target specific     germline B cell receptors. Science 340, 711-716. -   Jardine, J. G., Ota, T., Sok, D., Pauthner, M., Kulp, D. W.,     Kalyuzhniy, O., Skog, P. D., Thinnes, T. C., Bhullar, D., Briney,     B., et al. (2015). HIV-1 VACCINES. Priming a broadly neutralizing     antibody response to HIV-1 using a germline-targeting immunogen.     Science 349, 156-161. -   Keele, B. F., Giorgi, E. E., Salazar-Gonzalez, J. F., Decker, J. M.,     Pham, K. T., Salazar, M. G., Sun, C., Grayson, T., Wang, S., Li, H.,     et al. (2008). Identification and characterization of transmitted     and early founder virus envelopes in primary HIV-1 infection. Proc.     Natl. Acad. Sci. U.S.A. 105, 7552-7557. -   Kepler, T. B. (2013). Reconstructing a B-cell clonal lineage. I.     Statistical inference of unobserved ancestors. F1000Res 2, 103. -   Kepler, T. B., Munshaw, S., Wiehe, K., Zhang, R., Yu, J. S.,     Woods, C. W., Denny, T. N., Tomaras, G. D., Alam, S. M., Moody, M.     A., et al. (2014). Reconstructing a B-Cell Clonal Lineage. II.     Mutation, Selection, and Affinity Maturation. Front. Immunol. 5,     170. -   Klein, F., Diskin, R., Scheid, J. F., Gaebler, C., Mouquet, H.,     Georgiev, I. S., Pancera, M., Zhou, T., Incesu, R. B., Fu, B. Z., et     al. (2013). Somatic mutations of the immunoglobulin framework are     generally required for broad and potent HIV-1 neutralization. Cell     153, 126-138. -   Liao, H. X., Lynch, R., Zhou, T., Gao, F., Alam, S. M., Boyd, S. D.,     Fire, A. Z., Roskin, K. M., Schramm, C. A., Zhang, Z., et al.     (2013). Co-evolution of a broadly neutralizing HIV-1 antibody and     founder virus. Nature 496, 469-476. -   Liu, M., Yang, G., Wiehe, K., Nicely, N. I., Vandergrift, N. A.,     Rountree, W., Bonsignori, M., Alam, S. M., Gao, J., Haynes, B. F.,     et al. (2015). Polyreactivity and autoreactivity among HIV-1     antibodies. J. Virol. 89, 784-798. -   Mascola, J. R., and Haynes, B. F. (2013). HIV-1 neutralizing     antibodies: understanding nature's pathways. Immunol. Rev. 254,     225-244. -   McDonald, I. K., and Thornton, J. M. (1994). Satisfying hydrogen     bonding potential in proteins. J. Mol. Biol. 238, 777-793. -   McGuire, A. T., Hoot, S., Dreyer, A. M., Lippy, A., Stuart, A.,     Cohen, K. W., Jardine, J., Menis, S., Scheid, J. F., West, A. P., et     al. (2013). Engineering HIV envelope protein to activate germline B     cell receptors of broadly neutralizing anti-CD4 binding site     antibodies. J. Exp. Med. 210, 655-663. -   Otwinowski, Z., and Minor, W. (1997). Processing of X-ray     diffraction data collected in oscillation mode. Method Enzymol. 276,     307-326. -   Pugach, P., Ozorowski, G., Cupo, A., Ringe, R., Yasmeen, A., de Val,     N., Derking, R., Kim, H. J., Korzun, J., Golabek, M., et al. (2015).     A native-like SOSIP.664 trimer based on an HIV-1 subtype B env     gene. J. Virol. 89, 3380-3395. -   Rudicell, R. S., Do Kwon, Y., Ko, S. Y., Pegu, A., Louder, M. K.,     Georgiev, I. S., Wu, X. L., Zhu, J., Boyington, J. C., Chen, X. J.,     et al. (2014). Enhanced Potency of a Broadly Neutralizing HIV-1     Antibody In Vitro Improves Protection against Lentiviral Infection     In Vivo. J. Virol. 88, 12669-12682. -   Sanders, R. W., Derking, R., Cupo, A., Julien, J. P., Yasmeen, A.,     de Val, N., Kim, H. J., Blattner, C., de la Pena, A. T., Korzun, J.,     et al. (2013). A next-generation cleaved, soluble HIV-1 Env trimer,     BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly     neutralizing but not non-neutralizing antibodies. PLoS Pathog. 9,     e1003618. -   Scheid, J. F., Mouquet, H., Feldhahn, N., Seaman, M. S., Velinzon,     K., Pietzsch, J., Ott, R. G., Anthony, R. M., Zebroski, H., Hurley,     A., et al. (2009). Broad diversity of neutralizing antibodies     isolated from memory B cells in HIV-infected individuals. Nature     458, 636-640. -   Scheid, J. F., Mouquet, H., Ueberheide, B., Diskin, R., Klein, F.,     Oliveira, T. Y., Pietzsch, J., Fenyo, D., Abadir, A., Velinzon, K.,     et al. (2011). Sequence and structural convergence of broad and     potent HIV antibodies that mimic CD4 binding. Science 333,     1633-1637. -   Sui, Z. W., Chen, Q. J., Wu, R., Zhang, H. B., Zheng, M., Wang, H.     Z., and Chen, Z. (2010). Cross-protection against influenza virus     infection by intranasal administration of M2-based vaccine with     chitosan as an adjuvant. Arch. Virol. 155, 535-544. -   Verkoczy, L., Chen, Y., Zhang, J., Bouton-Verville, H., Newman, A.,     Lockwood, B., Scearce, R. M., Montefiori, D. C., Dennison, S. M.,     Xia, S. M., et al. (2013). Induction of HIV-1 broad neutralizing     antibodies in 2F5 knock-in mice: selection against membrane proximal     external region-associated autoreactivity limits T-dependent     responses. J. Immunol. 191, 2538-2550. -   Verkoczy, L., Diaz, M., Holl, T. M., Ouyang, Y. B., Bouton-Verville,     H., Alam, S. M., Liao, H. X., Kelsoe, G., and Haynes, B. F. (2010).     Autoreactivity in an HIV-1 broadly reactive neutralizing antibody     variable region heavy chain induces immunologic tolerance. Proc.     Natl. Acad. Sci. U.S.A. 107, 181-186. -   Verkoczy, L., Kelsoe, G., Moody, M. A., and Haynes, B. F. (2011).     Role of immune mechanisms in induction of HIV-1 broadly neutralizing     antibodies. Curr. Opin. Immunol. 23, 383-390. -   Wu, X., Yang, Z. Y., Li, Y., Hogerkorp, C. M., Schief, W. R.,     Seaman, M. S., Zhou, T., Schmidt, S. D., Wu, L., Xu, L., et al.     (2010). Rational design of envelope identifies broadly neutralizing     human monoclonal antibodies to HIV-1. Science 329, 856-861. -   Wu, X., Zhou, T., Zhu, J., Zhang, B., Georgiev, I., Wang, C., Chen,     X., Longo, N. S., Louder, M., McKee, K., et al. (2011). Focused     evolution of HIV-1 neutralizing antibodies revealed by structures     and deep sequencing. Science 333, 1593-1602. -   Yang, G., Holl, T. M., Liu, Y., Li, Y., Lu, X., Nicely, N. I.,     Kepler, T. B., Alam, S. M., Liao, H. X., Cain, D. W., et al. (2013).     Identification of autoantigens recognized by the 2F5 and 4E10     broadly neutralizing HIV-1 antibodies. J. Exp. Med. 210, 241-256. -   Zhou, T., Georgiev, I., Wu, X., Yang, Z. Y., Dai, K., Finzi, A.,     Kwon, Y. D., Scheid, J. F., Shi, W., Xu, L., et al. (2010).     Structural basis for broad and potent neutralization of HIV-1 by     antibody VRC01. Science 329, 811-817. -   Zhou, T., Lynch, R. M., Chen, L., Acharya, P., Wu, X.,     Doria-Rose, N. A., Joyce, M. G., Lingwood, D., Soto, C., Bailer, R.     T., et al. (2015). Structural Repertoire of HIV-1-Neutralizing     Antibodies Targeting the CD4 Supersite in 14 Donors. Cell 161,     1280-1292.

Example 9: HIV-1 Envelope Trimers and Other Envelope Designs

This example shows that stabilized HIV-1 Env trimer immunogens show enhanced antigenicity for broadly neutralizing antibodies, and are not recognized by non-neutralizing antibodies. See also FIGS. 22-25 and 61-74. The example also describes additional envelope modifications and designs. In some embodiments these envelopes, including but not limited to trimers are further multimerized, and/or used as particulate, high-density array in liposomes or other particles, for example but not limited to nanoparticles. Any one of the envelopes of the invention could be designed and expressed as described herein.

A stabilized chimeric SOSIP.III design was used to generate 10 CH505 trimers. The CH505 TF SOSIP.III bound the CH103 UCA. Binding affinity of the CH103 lineage to the CH505 TF SOSIP.III correlates with neutralization potency against CH505 TF virus. This design was applicable to diverse viruses from multiple clades.

These results indicate that the native trimer on virions could have initiated the CH103 lineage during natural infection. CH103 recognizes all three protomers on the Env trimer. The SOSIP.III mimicked the native trimer on the virion in that stronger binding to it correlated with neutralization potency for the CH103 lineage. The SOSIP.III design enables soluble mimics of the native trimer to be tested as sequential immunogens in CH505 B cell lineage design vaccination. These trimers enable our efforts to utilize B cell lineage design with trimeric immunogens.

Elicitation of neutralizing antibodies is one goal for antibody-based vaccines. Neutralizing antibodies target the native trimeric HIV-1 Env on the surface virions. The trimeric HIV-1 envelope protein consists of three protomers each containing a gp120 and gp41 heterodimer. Recent immunogen design efforts have generated soluble near-native mimics of the Env trimer that bind to neutralizing antibodies but not non-neutralizing antibodies. The recapitulation of the native trimer could be a key component of vaccine induction of neutralizing antibodies. Neutralizing Abs target the native trimeric HIV-1 Env on the surface of viruses (Poignard et al. J Virol. 2003 January; 77(1):353-65; Parren et al. J Virol. 1998 December; 72(12):10270-4; Yang et al. J Virol. 2006 November; 80(22):11404-8.). The HIV-1 Env protein consists of three protomers of gp120 and gp41 heterodimers that are noncovalently linked together (Center et al. J Virol. 2002 August; 76(15):7863-7.). Soluble near-native trimers preferentially bind neutralizing antibodies as opposed to non-neutralizing antibodies (Sanders et al. PLoS Pathog. 2013 September; 9(9): e1003618).

Sequential Env vaccination has elicited broad neutralization in the plasma of one macaque (Example 5A). The overall goal of our project is to increase the frequence of vaccine induction of bnabs in the plasma of primates with sequential Env vaccination. We hypothesized that vaccination with sequential immunogens that target bnAb B cell lineage and mimic native trimers will increase the frequency of broadly neutralizing plasma antibodies. One goal is increase the frequency of vaccine induction of bnAb in the plasma of primates by sequential Env vaccination. It is expected that vaccination with sequential immunogens that target bnAb B cell lineages and mimic the native trimers on virions will increase the frequency of broadly neutralizing plasma antibodies.

Previous work has shown that CH505 derived soluble trimers are hard to produce. From a study published by Julien et al in 2015 (Proc Natl Acad Sci USA. 2015 Sep. 22; 112(38): 11947-11952.) it was shown that while CH505 produced comparable amounts of protein by transient transfection, only 5% of the CH505 protein formed trimer which 5 times lower than the gold standard viral strain BG505. Provided here are non-limiting embodiments of well-folded trimers for Env immunizations.

Near-native soluble trimers using the 6R.SOSIP.664 design are capable of generating autologous tier 2 neutralizing plasma antibodies in the plasma (Sanders et al. 2015), which provides a starting point for designing immunogens to elicit broadly neutralizing antibodies. While these trimers are preferentially antigenic for neutralizing antibodies they still possess the ability to expose the V3 loop, which generally results in strain-specific binding and neutralizing antibodies after vaccination. Using the unliganded structure the BG505.6R.SOSIP.664 has been stabilized by adding cysteines at position 201 and 433 to constrain the conformational flexibility such that the V3 loop is maintained unexposed (Kwon et al. Nat Struct Mol Biol. 2015 July; 22(7): 522-531.).

Immunogen design. Provided are engineered trimeric immunogens derived from multiple viruses from CH505. We generated chimeric 6R.SOSIP.664, chimeric disulfide stabilized (DS) 6R.SOSIP.664 (Kwon et al Nat Struct Mol Biol. 2015 July; 22(7): 522-531.), chimeric 6R.SOSIP.664v4.1 (DeTaeye et al. Cell. 2015 Dec. 17; 163(7):1702-15. doi: 10.1016/j.cell.2015.11.056), and chimeric 6R.SOSIP.664v4.2 (DeTaeye et al. Cell. 2015 Dec. 17; 163(7):1702-15. doi: 10.1016/j.cell.2015.11.056). The 6R.SOSIP.664 is the basis for all of these designs and is made as a chimera of C.CH0505 and A.BG505. The gp120 of C.CH505 was fused with the BG505 inner domain gp120 sequence within the alpha helix 5 (a5) to result in the chimeric protein. The chimeric gp120 is disulfide linked to the A.BG505 gp41 as outlined by Sanders et al. (PLoS Pathog. 2013 September; 9(9): e1003618). These immunogens were designed as chimeric proteins that possess the BG505 gp41 connected to the CH505 gp120, since the BG505 strain is particularly adept at forming well-folded, closed trimers (FIG. 22A). This envelope design retains the CH505 CD4 binding site that is targeted by the CH103 and CH235 broadly neutralizing antibody lineages that were isolated from CH505.

FIGS. 22 and 23 show nucleic acid and amino acid and sequences of various CH505 envelope trimer designs. FIG. 23 B shows an annotated sequence of the SOSIP.III design. Based on the various SOSIP designs, any other suitable envelope, for example but not limited to CH505 envelopes as described in WO2014042669 can be designed.

Recombinant envelopes as trimers could be produced and purified by any suitable method. For a non-limiting example of purification methods see Ringe R P, Yasmeen A, Ozorowski G, Go E P, Pritchard L K, Guttman M, Ketas T A, Cottrell C A, Wilson I A, Sanders R W, Cupo A, Crispin M, Lee K K, Desaire H, Ward A B, Klasse P J, Moore J P. 2015. Influences on the design and purification of soluble, recombinant native-like HIV-1 envelope glycoprotein trimers. J Virol 89:12189-12210. doi:10.1128/JVI.01768-15.

Multimeric Envelopes

Presentation of antigens as particulates reduces the B cell receptor affinity necessary for signal transduction and expansion (See Baptista et al. EMBO J. 2000 Feb. 15; 19(4): 513-520). Displaying multiple copies of the antigen on a particle provides an avidity effect that can overcome the low affinity between the antigen and B cell receptor. The initial B cell receptor specific for pathogens can be low affinity, which precludes vaccines from being able to stimulate and expand B cells of interest. In particular, very few naïve B cells from which HIV-1 broadly neutralizing antibodies arise can bind to soluble HIV-1 Envelope. Provided are envelopes, including but not limited to trimers as particulate, high-density array on liposomes or other particles, for example but not limited to nanoparticles. See e.g. He et al. Nature Communications 7, Article number: 12041 (2016), doi:10.1038/ncomms12041; Bamrungsap et al. Nanomedicine, 2012, 7 (8), 1253-1271.

To improve the interaction between the naïve B cell receptor and CH505 SOSIP trimer protein we created to two constructs that can be presented on particles. The first construct was made by fusing HIV-1 Envelope trimer CH505 to ferritin (See FIG. 24G). Ferritin protein self assembles into a small nanoparticle with three fold axis of symmetry. At these axis CH505 envelope protein was fused. Therefore the assembly of the three-fold axis also clusters three HIV-1 envelope protomers together to form an envelope trimer. Each ferritin particle has 6 axises which equates to 6 CH505 trimers being displayed per particle. See e.g. Sliepen et al. Retrovirology 201512:82, DOI: 10.1186/s12977-015-0210-4; See also FIG. 24H-J.

Another approach to multimerize expression constructs uses Staphylococcus Sortase A transpeptidase ligation to conjugate CH505 envelope trimers to cholesterol. The CH505 trimers can then be embedded into liposomes via the conjugated cholesterol. To conjugate the CH505 trimer to cholesterol either a C-terminal LPXTG tag (SEQ ID NO: 396) or a N-terminal pentaglycine repeat tag (SEQ ID NO: 307) was added to the CH505 envelope trimer gene. Cholesterol was also synthesized with these two tags. Sortase A was then used to covalently bond the tagged CH505 envelope to the cholesterol. The sortase A-tagged trimer protein can also be used to conjugate the trimer to other peptides, proteins, or fluorescent labels.

The invention provides design of envelopes and trimer designs wherein the envelope comprises a linker which permits addition of a lipid, such as but not limited to cholesterol, via a Sortase A reaction. See e.g. Tsukiji, S. and Nagamune, T. (2009), Sortase-Mediated Ligation: A Gift from Gram-Positive Bacteria to Protein Engineering. ChemBioChem, 10: 787-798. doi:10.1002/cbic.200800724; Proft, T. Sortase-mediated protein ligation: an emerging biotechnology tool for protein modification and immobilisation. Biotechnol Lett (2010) 32: 1. doi:10.1007/s10529-009-0116-0; Lena Schmohl, Dirk Schwarzer, Sortase-mediated ligations for the site-specific modification of proteins, Current Opinion in Chemical Biology, Volume 22, October 2014, Pages 122-128, ISSN 1367-5931, dx.doi.org/10.1016/j.cbpa.2014.09.020; Tabata et al. Anticancer Res. 2015 August; 35(8):4411-7.

The lipid modified envelopes and trimers could be formulated as liposomes. Any suitable liposome composition is contemplated.

Non-limiting embodiments of envelope designs for use in Sortase A reaction are shown in FIG. 24 B-D.

Design of Trimers with Readthrough Codons

The development of clonal cell lines that highly express trimeric HIV-1 Envelope will facilitate manufacturing of high quality proteins for clinical and research purposes. However, it is challenging to identify the cells that express trimeric protein among the many cells making various forms of HIV-1 Envelope with in the cell population. To identify cells expressing trimeric HIV-1 Envelope protein, we designed an expression construct that simultaneously produces both secreted Envelope protein as well as membrane anchored Envelope protein. The secreted Envelope protein can be purified using standard methods and results in unaltered soluble envelope. The membrane-anchored Envelope protein serves to mark the cells within a population of cells that expresses trimeric Envelope. More specifically, the trimeric Envelope expressing cells are sorted by fluorescence-activated cell sorting using a HIV-1 trimer specific antibody. The sorted cells can then be used to initiate clonal populations of cells that have been phenotypically shown to express the protein of interest.

The expression construct is designed by taking advantage of the amber stop codon UAG in messenger RNA. The codon UAG usually signifies the end of the polypeptide sequence, but at a low rate the ribosome can readthrough this stop codon and continue to elongate the polypeptide chain. We incorporated this stop codon into our protein construct followed by the natural BG505 gp41 transmembrane and cytoplasmic tail sequence ended with two stop codons. Therefore, when the stop codon is readthrough a membrane-anchored gp120/gp41 heterodimer is formed. Loughran et al. (2014) identified that the efficiency of readthrough could be increased by flanking the amber stop codon with the nucleotides CTA. Readthrough could be even further augmented with the addition of CTAG nucleotides after the amber stop codon. We engineered expression constructs with both modifications to ensure an optimal ratio of membrane-anchored and secreted trimeric Envelope protein. Since the CTAG creates a shift in reading frame we added GC nucleotides after the CTAG motif to preserve the original reading frame. The addition of CTAGGC results in the membrane anchored protein having a leucine and glycine residue expressed before the transmembrane domain. FIG. 24A shows non-limiting examples of readthrough designs. FIG. 24E and FIG. 24F show expression of “CTA” and “CTAGGC” designs in transiently transfected 293F cells. Any one of the envelopes of the invention could be designed and expressed as readthrough envelopes. 

What is claimed is:
 1. A recombinant HIV-1 envelope polypeptide comprising all the consecutive amino acids after the signal peptide in HIV-1 envelope CH505TFchim.6R.SOSIP.664v4.1 (SEQ ID NO:260), CH505M5chim.6R.SOSIP.664v4.1 (SEQ ID NO:242), CH505M11chim.6R.SOSIP.664v4.1 (SEQ ID NO:244), CH505w20.14chim.6R.SOSIP.664v4.1 (SEQ ID NO:254), CH505w30.20.chim.6R.SOSIP.664v4.1 (SEQ ID NO:258), CH505w30.12chim.6R.SOSIP.664v4.1 (SEQ ID NO:256), or CH505w136.B18chim.6R.SOSIP.664v4.1 (SEQ ID NO:252).
 2. A recombinant trimer comprising three identical polypeptides of claim
 1. 3. An immunogenic composition comprising the recombinant trimer of claim 2 and a carrier.
 4. The composition of claim 3 further comprising an adjuvant.
 5. The recombinant trimer of claim 2 comprising three polypeptides, each polypeptide comprising all the consecutive amino acids after the signal peptide in HIV-1 envelope CH505TFchim.6R.SOSIP644v4.1 (SEQ ID NO:260).
 6. An immunogenic composition comprising the recombinant trimer of claim 5 and a carrier.
 7. The immunogenic composition of claim 6 further comprising an adjuvant.
 8. The recombinant trimer of claim 5, wherein the trimer is comprised in a nanoparticle.
 9. The recombinant trimer of claim 2, wherein the trimer is comprised in a nanoparticle.
 10. A method of inducing an immune response in a subject comprising administering a composition comprising a recombinant HIV-1 envelope polypeptide comprising all the consecutive amino acids after the signal peptide in HIV-1 envelope CH505TFchim.6R.SOSIP.664v4.1 (SEQ ID NO:260), CH505M5chim.6R.SOSIP.664v4.1 (SEQ ID NO:242), CH505M11chim.6R.SOSIP.664v4.1 (SEQ ID NO:244), CH505w20.14chim.6R.SOSIP.664v4.1 (SEQ ID NO:254), CH505w30.20.chim.6R.SOSIP.664v4.1 (SEQ ID NO:258), CH505w30.12chim.6R.SOSIP.664v4.1 (SEQ ID NO:256), or CH505w136.B18chim.6R.SOSIP.664v4.1 (SEQ ID NO:252).
 11. The method of 10, wherein the composition comprises a recombinant trimer comprising three identical polypeptides of claim
 10. 12. The method of claim 11, comprising administering HIV-1 polypeptides CH505TFchim.6R.SOSIP.664v4.1 (SEQ ID NO:260) as the recombinant trimer.
 13. The method of claim 12, wherein the CH505TFchim.6R.SOSIP.664v4.1 (SEQ ID NO:260) recombinant trimer is administered as a nanoparticle.
 14. The method of claim 10, wherein the composition further comprises a carrier.
 15. The method of claim 14, further comprising administering an adjuvant.
 16. The method of claim 10, further comprising administering a nucleic acid encoding CH5050TFchim.6R.SOSIP.664v4.1 (SEQ ID NO:260). 